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Zhydzetski A, Głowacka-Grzyb Z, Bukowski M, Żądło T, Bonar E, Władyka B. Agents Targeting the Bacterial Cell Wall as Tools to Combat Gram-Positive Pathogens. Molecules 2024; 29:4065. [PMID: 39274911 PMCID: PMC11396672 DOI: 10.3390/molecules29174065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/16/2024] Open
Abstract
The cell wall is an indispensable element of bacterial cells and a long-known target of many antibiotics. Penicillin, the first discovered beta-lactam antibiotic inhibiting the synthesis of cell walls, was successfully used to cure many bacterial infections. Unfortunately, pathogens eventually developed resistance to it. This started an arms race, and while novel beta-lactams, either natural or (semi)synthetic, were discovered, soon upon their application, bacteria were developing resistance. Currently, we are facing the threat of losing the race since more and more multidrug-resistant (MDR) pathogens are emerging. Therefore, there is an urgent need for developing novel approaches to combat MDR bacteria. The cell wall is a reasonable candidate for a target as it differentiates not only bacterial and human cells but also has a specific composition unique to various groups of bacteria. This ensures the safety and specificity of novel antibacterial agents that target this structure. Due to the shortage of low-molecular-weight candidates for novel antibiotics, attention was focused on peptides and proteins that possess antibacterial activity. Here, we describe proteinaceous agents of various origins that target bacterial cell wall, including bacteriocins and phage and bacterial lysins, as alternatives to classic antibiotic candidates for antimicrobial drugs. Moreover, advancements in protein chemistry and engineering currently allow for the production of stable, specific, and effective drugs. Finally, we introduce the concept of selective targeting of dangerous pathogens, exemplified by staphylococci, by agents specifically disrupting their cell walls.
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Affiliation(s)
- Aliaksandr Zhydzetski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Zuzanna Głowacka-Grzyb
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza St. 11, 30-348 Cracow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Tomasz Żądło
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza St. 11, 30-348 Cracow, Poland
| | - Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Benedykt Władyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
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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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Tan Z, Tezuka T, Ohnishi Y. Identification of a putative cell wall-hydrolyzing amidase involved in sporangiospore maturation in Actinoplanes missouriensis. J Bacteriol 2024; 206:e0045623. [PMID: 38426722 PMCID: PMC10955841 DOI: 10.1128/jb.00456-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Actinoplanes missouriensis is a filamentous bacterium that differentiates into terminal sporangia, each containing a few hundred spores. Previously, we reported that a cell wall-hydrolyzing N-acetylglucosaminidase, GsmA, is required for the maturation process of sporangiospores in A. missouriensis; sporangia of the gsmA null mutant (ΔgsmA) strain released chains of 2-20 spores under sporangium dehiscence-inducing conditions. In this study, we identified and characterized a putative cell wall hydrolase (AsmA) that is also involved in sporangiospore maturation. AsmA was predicted to have a signal peptide for the general secretion pathway and an N-acetylmuramoyl-l-alanine amidase domain. The transcript level of asmA increased during the early stages of sporangium formation. The asmA null mutant (ΔasmA) strain showed phenotypes similar to those of the wild-type strain, but sporangia of the ΔgsmAΔasmA double mutant released longer spore chains than those from the ΔgsmA sporangia. Furthermore, a weak interaction between AsmA and GsmA was detected in a bacterial two-hybrid assay using Escherichia coli as the host. Based on these results, we propose that AsmA is an enzyme that hydrolyzes peptidoglycan at septum-forming sites to separate adjacent spores during sporangiospore maturation in cooperation with GsmA in A. missouriensis.IMPORTANCEActinoplanes missouriensis produces sporangiospores as dormant cells. The spores inside the sporangia are assumed to be formed from prespores generated by the compartmentalization of intrasporangium hyphae via septation. Previously, we identified GsmA as a cell wall hydrolase responsible for the separation of adjacent spores inside sporangia. However, we predicted that an additional cell wall hydrolase(s) is inevitably involved in the maturation process of sporangiospores because the sporangia of the gsmA null mutant strain released not only tandemly connected spore chains (2-20 spores) but also single spores. In this study, we successfully identified a putative cell wall hydrolase (AsmA) that is involved in sporangiospore maturation in A. missouriensis.
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Affiliation(s)
- Zhuwen Tan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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Pitkänen I, Tossavainen H, Permi P. 1H, 13C, and 15N NMR chemical shift assignment of LytM N-terminal domain (residues 26-184). BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:257-263. [PMID: 37742292 PMCID: PMC10630248 DOI: 10.1007/s12104-023-10151-5] [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: 07/10/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023]
Abstract
Antibiotic resistance is a growing problem and a global threat for modern healthcare. New approaches complementing the traditional antibiotic drugs are urgently needed to secure the ability to treat bacterial infections also in the future. Among the promising alternatives are bacteriolytic enzymes, such as the cell wall degrading peptidoglycan hydrolases. Staphylococcus aureus LytM, a Zn2+-dependent glycyl-glycine endopeptidase of the M23 family, is one of the peptidoglycan hydrolases. It has a specificity towards staphylococcal peptidoglycan, making it an interesting target for antimicrobial studies. LytM hydrolyses the cell wall of S. aureus, a common pathogen with multi-resistant strains that are difficult to treat, such as the methicillin-resistant S. aureus, MRSA. Here we report the 1H, 15N and 13C chemical shift assignments of S. aureus LytM N-terminal domain and linker region, residues 26-184. These resonance assignments can provide the basis for further studies such as elucidation of structure and interactions.
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Affiliation(s)
- Ilona Pitkänen
- Department of Biological and Environmental Science, University of Jyvaskyla, FI-40014, Jyvaskyla, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyvaskyla, FI-40014, Jyvaskyla, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyvaskyla, FI-40014, Jyvaskyla, Finland.
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, FI-40014, Jyvaskyla, Finland.
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland.
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Charoenjotivadhanakul S, Sakdee S, Imtong C, Li HC, Angsuthanasombat C. Conserved loop residues-Tyr 270 and Asn 372 near the catalytic site of the lysostaphin endopeptidase are essential for staphylolytic activity toward pentaglycine binding and catalysis. Biochem Biophys Res Commun 2023; 668:111-117. [PMID: 37245291 DOI: 10.1016/j.bbrc.2023.05.085] [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: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Lysostaphin endopeptidase cleaves pentaglycine cross-bridges found in staphylococcal cell-wall peptidoglycans and proves very effective in combatting methicillin-resistant Staphylococcus aureus. Here, we revealed the functional importance of two loop residues, Tyr270 in loop 1 and Asn372 in loop 4, which are highly conserved among the M23 endopeptidase family and are found close to the Zn2+-coordinating active site. Detailed analyses of the binding groove architecture together with protein-ligand docking showed that these two loop residues potentially interact with the docked ligand-pentaglycine. Ala-substituted mutants (Y270A and N372A) were generated and over-expressed in Escherichia coli as a soluble form at levels comparable to the wild type. A drastic decrease in staphylolytic activity against S. aureus was observed for both mutants, suggesting an essential role of the two loop residues in lysostaphin function. Further substitutions with an uncharged polar Gln side-chain revealed that only the Y270Q mutation caused a dramatic reduction in bioactivity. In silico predicting the effect of binding site mutations revealed that all mutations displayed a large ΔΔGbind value, signifying requirements of the two loop residues for efficient binding to pentaglycine. Additionally, MD simulations revealed that Y270A and Y270Q mutations induced large flexibility of the loop 1 region, showing markedly increased RMSF values. Further structural analysis suggested that Tyr270 conceivably participated in the oxyanion stabilization of the enzyme catalysis. Altogether, our present study disclosed that two highly conserved loop residues, loop 1-Tyr270 and loop 4-Asn372, located near the lysostaphin active site are crucially involved in staphylolytic activity toward binding and catalysis of pentaglycine cross-links.
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Affiliation(s)
- Sathapat Charoenjotivadhanakul
- Bacterial Toxin Research Innovation Laboratory, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Somsri Sakdee
- Bacterial Toxin Research Innovation Laboratory, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Chompounoot Imtong
- Laboratory of Cell Chemical Biology, Biophysics Institute for Research and Development (BIRD), Chiang Mai, 50110, Thailand
| | - Hui-Chun Li
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, 97004, Taiwan
| | - Chanan Angsuthanasombat
- Bacterial Toxin Research Innovation Laboratory, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand; Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, 97004, Taiwan; Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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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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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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Structural and Functional Characterization of β-lytic Protease from Lysobacter capsici VKM B-2533 T. Int J Mol Sci 2022; 23:ijms232416100. [PMID: 36555752 PMCID: PMC9783410 DOI: 10.3390/ijms232416100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The crystal structure of the Lysobacter capsici VKM B-2533T β-lytic protease (Blp), a medicinally promising antimicrobial enzyme, was first solved. Blp was established to possess a folding characteristic of the M23 protease family. The groove of the Blp active site, as compared with that of the LasA structural homologue from Pseudomonas aeruginosa, was found to have amino acid differences. Biochemical analysis revealed no differences in the optimal reaction conditions for manifesting Blp and LasA bacteriolytic activities. At the same time, Blp had a broader range of action against living and autoclaved target cells. The results suggest that the distinction in the geometry of the active site and the charge of amino acid residues that form the active site groove can be important for the hydrolysis of different peptidoglycan types in target cells.
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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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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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Wysocka A, Łężniak Ł, Jagielska E, Sabała I. Electrostatic Interaction with the Bacterial Cell Envelope Tunes the Lytic Activity of Two Novel Peptidoglycan Hydrolases. Microbiol Spectr 2022; 10:e0045522. [PMID: 35467396 PMCID: PMC9241647 DOI: 10.1128/spectrum.00455-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/04/2022] [Indexed: 12/14/2022] Open
Abstract
Peptidoglycan (PG) hydrolases, due to their crucial role in the metabolism of the bacterial cell wall (CW), are increasingly being considered suitable targets for therapies, and a potent alternative to conventional antibiotics. In the light of contradictory data reported, detailed mechanism of regulation of enzymes activity based on electrostatic interactions between hydrolase molecule and bacterial CW surface remains unknown. Here, we report a comprehensive study on this phenomenon using as a model two novel PG hydrolases, SpM23_A, and SpM23_B, which although share the same bacterial host, similarities in sequence conservation, domain architecture, and structure, display surprisingly distinct net charges (in 2D electrophoresis, pI 6.8, and pI 9.7, respectively). We demonstrate a strong correlation between hydrolases surface net charge and the enzymes activity by modulating the charge of both, enzyme molecule and bacterial cell surface. Teichoic acids, anionic polymers present in the bacterial CW, are shown to be involved in the mechanism of enzymes activity regulation by the electrostatics-based interplay between charged bacterial envelope and PG hydrolases. These data serve as a hint for the future development of chimeric PG hydrolases of desired antimicrobial specificity. IMPORTANCE This study shows direct relationship between the surface charge of two recently described enzymes, SpM23_A and SpM23_B, and bacterial cell walls. We demonstrate that by (i) surface charge probing of bacterial strains collection, (ii) reduction of the net charge of the positively charged enzyme, and (iii) altering the net charge of the bacterial surface by modifying the content and composition of teichoic acids. In all cases, we observed that lytic activity and binding strength of SpM23 enzymes, are regulated by electrostatic interactions with the bacterial cell envelope and that this interaction contributes to the determination of the spectrum of susceptible bacterial species. Moreover, we revealed the regulatory role of charged cell wall components, namely, teichoic and lipoteichoic acids, over the SpM23 enzymes. We believe that our findings make an important contribution to understand the means of hydrolases activity regulation in the complex environment of the bacterial cell wall.
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Affiliation(s)
- Alicja Wysocka
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Łukasz Łężniak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Jagielska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - Izabela Sabała
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
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12
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Wang M, Buist G, van Dijl JM. Staphylococcus aureus cell wall maintenance - the multifaceted roles of peptidoglycan hydrolases in bacterial growth, fitness, and virulence. FEMS Microbiol Rev 2022; 46:6604383. [PMID: 35675307 PMCID: PMC9616470 DOI: 10.1093/femsre/fuac025] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/22/2022] [Accepted: 05/25/2022] [Indexed: 01/07/2023] Open
Abstract
Staphylococcus aureus is an important human and livestock pathogen that is well-protected against environmental insults by a thick cell wall. Accordingly, the wall is a major target of present-day antimicrobial therapy. Unfortunately, S. aureus has mastered the art of antimicrobial resistance, as underscored by the global spread of methicillin-resistant S. aureus (MRSA). The major cell wall component is peptidoglycan. Importantly, the peptidoglycan network is not only vital for cell wall function, but it also represents a bacterial Achilles' heel. In particular, this network is continuously opened by no less than 18 different peptidoglycan hydrolases (PGHs) encoded by the S. aureus core genome, which facilitate bacterial growth and division. This focuses attention on the specific functions executed by these enzymes, their subcellular localization, their control at the transcriptional and post-transcriptional levels, their contributions to staphylococcal virulence and their overall importance in bacterial homeostasis. As highlighted in the present review, our understanding of the different aspects of PGH function in S. aureus has been substantially increased over recent years. This is important because it opens up new possibilities to exploit PGHs as innovative targets for next-generation antimicrobials, passive or active immunization strategies, or even to engineer them into effective antimicrobial agents.
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Affiliation(s)
- Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO Box 30001, 9700 RB Groningen, the Netherlands
| | | | - Jan Maarten van Dijl
- Corresponding author: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. box 30001, HPC EB80, 9700 RB Groningen, the Netherlands, Tel. +31-50-3615187; Fax. +31-50-3619105; E-mail:
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Costa SS, Lago LAB, Silva A, Graças DAD, Lameira J, Baraúna RA. Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin. Genet Mol Biol 2022; 45:e20210204. [PMID: 35037933 PMCID: PMC8762718 DOI: 10.1590/1678-4685-gmb-2021-0204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/05/2021] [Indexed: 11/22/2022] Open
Abstract
Bacteriocins are antimicrobial peptides expressed by bacteria through ribosomal activity. In this study, we analyzed the diversity of bacteriocin-like genes in the Tucuruí-HPP using a whole-metagenome shotgun sequencing approach. Three layers of the water column were analyzed (photic, aphotic and sediment). Detection of bacteriocin-like genes was performed with blastx using the BAGEL4 database as subject sequences. In order to calculate the abundance of bacteriocin-like genes we also determined the number of 16S rRNA genes using blastn. Taxonomic analysis was performed using RAST server and the metagenome was assembled using IDBA-UD in order to recover the full sequence of a zoocin which had its three-dimensional structure determined. The photic zone presented the highest number of reads affiliated to bacteriocins. The most abundant bacteriocins were sonorensin, Klebicin D , pyocin and colicin. The zoocin model was composed of eight anti-parallel β-sheets and two α-helices with a Zn2+ ion in the active site. This model was considerably stable during 10 ns of molecular dynamics simulation. We observed a high diversity of bacteriocins in the Tucuruí-HPP, demonstrating that the environment is an inexhaustible source for prospecting these molecules. Finally, the zoocin model can be used for further studies of substrate binding and molecular mechanisms involving peptidoglycan degradation.
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Affiliation(s)
- Sávio S Costa
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
| | - Leticia A B Lago
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
| | - Artur Silva
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
| | - Diego A das Graças
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
| | - Jerônimo Lameira
- Universidade Federal do Pará, Instituto de Ciências Exatas e Naturais, Laboratório de Planejamento e Desenvolvimento de Fármacos, Belém, PA, Brazil
| | - Rafael A Baraúna
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
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14
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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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15
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Wang M, van den Berg S, Mora Hernández Y, Visser AH, Vera Murguia E, Koedijk DGAM, Bellink C, Bruggen H, Bakker-Woudenberg IAJM, van Dijl JM, Buist G. Differential binding of human and murine IgGs to catalytic and cell wall binding domains of Staphylococcus aureus peptidoglycan hydrolases. Sci Rep 2021; 11:13865. [PMID: 34226629 PMCID: PMC8257689 DOI: 10.1038/s41598-021-93359-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/28/2021] [Indexed: 12/27/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen causing high morbidity and mortality. Since multi-drug resistant S. aureus lineages are nowadays omnipresent, alternative tools for preventive or therapeutic interventions, like immunotherapy, are urgently needed. However, there are currently no vaccines against S. aureus. Surface-exposed and secreted proteins are regarded as potential targets for immunization against S. aureus infections. Yet, many potential staphylococcal antigens of this category do not elicit protective immune responses. To obtain a better understanding of this problem, we compared the binding of serum IgGs from healthy human volunteers, highly S. aureus-colonized patients with the genetic blistering disease epidermolysis bullosa (EB), or immunized mice to the purified S. aureus peptidoglycan hydrolases Sle1, Aly and LytM and their different domains. The results show that the most abundant serum IgGs from humans and immunized mice target the cell wall-binding domain of Sle1, and the catalytic domains of Aly and LytM. Interestingly, in a murine infection model, these particular IgGs were not protective against S. aureus bacteremia. In contrast, relatively less abundant IgGs against the catalytic domain of Sle1 and the N-terminal domains of Aly and LytM were almost exclusively detected in sera from EB patients and healthy volunteers. These latter IgGs may contribute to the protection against staphylococcal infections, as previous studies suggest that serum IgGs protect EB patients against severe S. aureus infection. Together, these observations focus attention on the use of particular protein domains for vaccination to direct potentially protective immune responses towards the most promising epitopes within staphylococcal antigens.
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Affiliation(s)
- Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Sanne van den Berg
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yaremit Mora Hernández
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Aafke Hinke Visser
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Elias Vera Murguia
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Dennis G A M Koedijk
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Channah Bellink
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Hilde Bruggen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Irma A J M Bakker-Woudenberg
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands.
| | - Girbe Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
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16
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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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17
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Chen K, Ojha SC, Imtong C, Linn AK, Li HC, Thonabulsombat C, Angsuthanasombat C. Molecular Insights into Zn 2+ Inhibition of the Antibacterial Endopeptidase Lysostaphin from Staphylococcus simulans. Protein Pept Lett 2021; 28:140-148. [PMID: 32533816 DOI: 10.2174/0929866527666200613221359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mature lysostaphin (~28-kDa Lss) from Staphylococcus simulans proves effective in killing methicillin-resistant Staphylococcus aureus (MRSA) which is endemic in hospitals worldwide. Lss is Zn2+-dependent endopeptidase, but its bacteriolytic activity could be affected by exogenously added Zn2+. OBJECTIVE To gain greater insights into structural and functional impacts of Zn2+and Ni2+on Lss-induced bioactivity. METHODS Lss purified via immobilized metal ion-affinity chromatography was assessed for bioactivity using turbidity reduction assays. Conformational change of metal ion-treated Lss was examined by circular dichroism and intrinsic fluorescence spectroscopy. Co-sedimentation assay was performed to study interactions between Zn2+-treated Lss and S. aureus peptidoglycans. Metal ionbinding prediction and intermolecular docking were used to locate an extraneous Zn2+-binding site. RESULTS A drastic decrease in Lss bioactivity against S. aureus and MRSA was revealed only when treated with Zn2+, but not Ni2+, albeit no negative effect of diethyldithiocarbamate-Zn2+-chelator on Lss-induced bioactivity. No severe conformational change was observed for Lss incubated with exogenous Zn2+ or Ni2+. Lss pre-treated with Zn2+ efficiently bound to S. aureus cell-wall peptidoglycans, suggesting non-interfering effect of exogenous metal ions on cell-wall targeting (CWT) activity. In silico analysis revealed that exogenous Zn2+, but not Ni2+, preferably interacted with a potential extraneous Zn2+-binding site (His253, Glu318 and His323) placed near the Zn2+-coordinating Lssactive site within the catalytic (CAT) domain. CONCLUSION Our present data signify the adverse influence of exogenous Zn2+ ions on Lss-induced staphylolytic activity through the exclusive presence within the CAT domain of an extraneous inhibitory Zn2+-binding site, without affecting the CWT activity.
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Affiliation(s)
- Ke Chen
- Department of Anatomy, Faculty of Science, Mahidol University, Payatai Campus, Bangkok, Thailand
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affliliated Hospital of Southwest Medical University, Luzhou, China
| | - Chompounoot Imtong
- Division of Biology, Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Pattani, Thailand
| | - Aung Khine Linn
- Laboratory of Synthetic Biophysics and Chemical Biology, Biophysics Institute for Research and Development (BIRD), Chiang Mai, Thailand
| | - Hui-Chun Li
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, Taiwan
| | | | - Chanan Angsuthanasombat
- Laboratory of Synthetic Biophysics and Chemical Biology, Biophysics Institute for Research and Development (BIRD), Chiang Mai, Thailand
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18
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Devlin H, Fulaz S, Hiebner DW, O’Gara JP, Casey E. Enzyme-Functionalized Mesoporous Silica Nanoparticles to Target Staphylococcus aureus and Disperse Biofilms. Int J Nanomedicine 2021; 16:1929-1942. [PMID: 33727807 PMCID: PMC7954034 DOI: 10.2147/ijn.s293190] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/09/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Staphylococcus aureus biofilms pose a unique challenge in healthcare due to their tolerance to a wide range of antimicrobial agents. The high cost and lengthy timeline to develop novel therapeutic agents have pushed researchers to investigate the use of nanomaterials to deliver antibiofilm agents and target biofilm infections more efficiently. Previous studies have concentrated on improving the efficacy of antibiotics by deploying nanoparticles as nanocarriers. However, the dispersal of the extracellular polymeric substance (EPS) matrix in biofilm-associated infections is also critical to the development of novel nanoparticle-based therapies. METHODS This study evaluated the efficacy of enzyme-functionalized mesoporous silica nanoparticles (MSNs) against methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) biofilms. MSNs were functionalized with the enzyme lysostaphin, which causes cell lysis of S. aureus bacteria. This was combined with two other enzyme functionalized MSNs, serrapeptase and DNase I which will degrade protein and eDNA in the EPS matrix, to enhance eradication of the biofilm. Cell viability after treatment with enzyme-functionalized MSNs was assessed using a MTT assay and CLSM, while crystal violet staining was used to assess EPS removal. RESULTS The efficacy of all three enzymes against S. aureus cells and biofilms was significantly improved when they were immobilized onto MSNs. Treatment efficacy was further enhanced when the three enzymes were used in combination against both MRSA and MSSA. Regardless of biofilm maturity (24 or 48 h), near-complete dispersal and killing of MRSA biofilms were observed after treatment with the enzyme-functionalized MSNs. Disruption of mature MSSA biofilms with a polysaccharide EPS was less efficient, but cell viability was significantly reduced. CONCLUSION The combination of these three enzymes and their functionalization onto nanoparticles might extend the therapeutic options for the treatment of S. aureus infections, particularly those with a biofilm component.
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Affiliation(s)
- Henry Devlin
- UCD School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Stephanie Fulaz
- UCD School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Dishon Wayne Hiebner
- UCD School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - James P O’Gara
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Eoin Casey
- UCD School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
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19
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Polak Y, Speth RC. Metabolism of angiotensin peptides by angiotensin converting enzyme 2 (ACE2) and analysis of the effect of excess zinc on ACE2 enzymatic activity. Peptides 2021; 137:170477. [PMID: 33400951 PMCID: PMC7887068 DOI: 10.1016/j.peptides.2020.170477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/21/2020] [Accepted: 12/15/2020] [Indexed: 01/02/2023]
Abstract
After decades of notoriety for its adverse cardiovascular, proinflammatory and profibrotic actions, the renin-angiotensin system (RAS) began to be cast in a more favorable light with the discovery of angiotensin-converting enzyme-2 (ACE2) in 2000. This monocarboxypeptidase, best known for its ability to metabolize angiotensin (Ang) II to Ang 1-7, counteracts the adverse effects of Ang II mediated by the AT1 Ang II receptor. Ang peptides are classically considered to be metabolized by aminopeptidases, by which the nomenclature Ang III (des-Asp1Ang II, 2-8 heptapeptide) and Ang IV (des-Asp1des-Arg2Ang II, 3-8 hexapeptide) are derived. This report compares the ability of recombinant human ACE2 (rhACE2) to metabolize Ang III, Ang IV and Ang V, (4-8 pentapeptide) relative to Ang II to form corresponding des-omega-Phe metabolites. rhACE2 has highest affinity (lowest Km) for Ang III, followed by Ang II ∼ Ang V, followed by Ang IV. However, rhACE2 has the highest Kcat for metabolising Ang IV followed by Ang V, Ang III and Ang II. The enzymatic efficiency (Kcat/Km) is highest for Ang V and Ang III followed by Ang IV and is lowest for Ang II. As a gluzincin metallopeptidase, ACE2 requires a zinc molecule at its active site for catalysis. This report also documents inhibition of ACE2 activity by concentrations of zinc exceeding 10 μM. These observations extend the functional significance of ACE2 to include the metabolic inactivation of Ang III, Ang IV and Ang V, reemphasizing the importance of monitoring zinc intake to maintain metabolic homeostasis.
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Affiliation(s)
- Yasmin Polak
- College of Pharmacy, University of Utrecht, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands; College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, 33328, United States.
| | - Robert C Speth
- College of Pharmacy, University of Utrecht, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands; College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, 33328, United States.
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20
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A Simple Protocol for the Determination of Lysostaphin Enzymatic Activity. Antibiotics (Basel) 2020; 9:antibiotics9120917. [PMID: 33348544 PMCID: PMC7766845 DOI: 10.3390/antibiotics9120917] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 11/29/2022] Open
Abstract
Antibacterial lysins are enzymes that hydrolyze bacterial peptidoglycan, which results in the rapid death of bacterial cells due to osmotic lysis. Lysostaphin is one of the most potent and well-studied lysins active against important nosocomial pathogen Staphylococcus aureus. Similarly to most other lysins, lysostaphin is composed of enzymatic and peptidoglycan-binding domains, and both domains influence its antibacterial activity. It is thus desirable to be able to study the activity of both domains independently. Lysostaphin cleaves pentaglycine cross-bridges within the staphylococcal peptidoglycan. Here, we report the protocol to study the catalytic activity of lysostaphin on the isolated pentaglycine peptide that is based on the chromogenic reaction of peptide amino groups with ninhydrin. Unlike previously reported assays, this protocol does not require in-house chemical synthesis or specialized equipment and can be readily performed in most laboratories. We demonstrate the use of this protocol to study the effect of EDTA treatment on the lysostaphin enzymatic activity. We further used this protocol to determine the catalytic efficiency of lysostaphin on the isolated pentaglycine and compared it to the apparent catalytic efficiency on the whole staphylococcal cells. These results highlight the relative impact of enzymatic and peptidoglycan-binding domains of lysostaphin on its bacteriolytic activity.
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21
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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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22
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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: 29] [Impact Index Per Article: 4.8] [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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23
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Chandra Ojha S, Imtong C, Meetum K, Sakdee S, Katzenmeier G, Angsuthanasombat C. Purification and characterization of the antibacterial peptidase lysostaphin from Staphylococcus simulans : Adverse influence of Zn 2+ on bacteriolytic activity. Protein Expr Purif 2018; 151:106-112. [DOI: 10.1016/j.pep.2018.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023]
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24
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Nahar S, Mizan MFR, Ha AJW, Ha SD. Advances and Future Prospects of Enzyme-Based Biofilm Prevention Approaches in the Food Industry. Compr Rev Food Sci Food Saf 2018; 17:1484-1502. [DOI: 10.1111/1541-4337.12382] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/22/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Shamsun Nahar
- Dept. of Food Science and Technology; Chung-Ang Univ.; Anseong Gyeonggi-Do 456-756 Republic of Korea
| | | | - Angela Jie-won Ha
- Dept. of Food Science and Technology; Chung-Ang Univ.; Anseong Gyeonggi-Do 456-756 Republic of Korea
| | - Sang-Do Ha
- Dept. of Food Science and Technology; Chung-Ang Univ.; Anseong Gyeonggi-Do 456-756 Republic of Korea
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25
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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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Arolas JL, Goulas T, Cuppari A, Gomis-Rüth FX. Multiple Architectures and Mechanisms of Latency in Metallopeptidase Zymogens. Chem Rev 2018; 118:5581-5597. [PMID: 29775286 DOI: 10.1021/acs.chemrev.8b00030] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metallopeptidases cleave polypeptides bound in the active-site cleft of catalytic domains through a general base/acid mechanism. This involves a solvent molecule bound to a catalytic zinc and general regulation of the mechanism through zymogen-based latency. Sixty reported structures from 11 metallopeptidase families reveal that prosegments, mostly N-terminal of the catalytic domain, block the cleft regardless of their size. Prosegments may be peptides (5-14 residues), which are only structured within the zymogens, or large moieties (<227 residues) of one or two folded domains. While some prosegments globally shield the catalytic domain through a few contacts, others specifically run across the cleft in the same or opposite direction as a substrate, making numerous interactions. Some prosegments block the zinc by replacing the solvent with particular side chains, while others use terminal α-amino or carboxylate groups. Overall, metallopeptidase zymogens employ disparate mechanisms that diverge even within families, which supports that latency is less conserved than catalysis.
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Affiliation(s)
- Joan L Arolas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Theodoros Goulas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Anna Cuppari
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
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