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Martinez-Bond EA, Soriano BM, Williams AH. The mechanistic landscape of Lytic transglycosylase as targets for antibacterial therapy. Curr Opin Struct Biol 2022; 77:102480. [PMID: 36323133 DOI: 10.1016/j.sbi.2022.102480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/24/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
Lytic transglycosylases (Ltgs) are glycan strand cleaving enzymes whose role is poorly understood in the genesis of the bacterial envelope. They play multiple roles in all stages of a bacterial life cycle, by creating holes in the peptidoglycan that is necessary for cell division and separation. Here, we review recent advances in understanding the suitability of Ltgs as antibacterial drug targets. We specifically highlight a known inhibitor bulgecin A that is able to inhibit the function of structurally diverse Ltgs, as well as synergize with beta-lactams to improve its efficacy in antibiotic insensitive strains. Discovery of new antibiotics or new targets has been challenging. These studies could provide a viable path toward designing broad-spectrum inhibitors that targets Ltgs.
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Affiliation(s)
- Elizabeth A Martinez-Bond
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA. https://twitter.com/bondlizbond
| | - Berliza M Soriano
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA. https://twitter.com/AWilliamslab
| | - Allison H Williams
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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2
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Turupcu A, Bowen AM, Di Paolo A, Matagne A, Oostenbrink C, Redfield C, Smith LJ. An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose. Proteins 2020; 88:82-93. [PMID: 31294851 PMCID: PMC6916166 DOI: 10.1002/prot.25770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 02/06/2023]
Abstract
The X-ray structure of lysozyme from bacteriophage lambda (λ lysozyme) in complex with the inhibitor hexa-N-acetylchitohexaose (NAG6) (PDB: 3D3D) has been reported previously showing sugar units from two molecules of NAG6 bound in the active site. One NAG6 is bound with four sugar units in the ABCD sites and the other with two sugar units in the E'F' sites potentially representing the cleavage reaction products; each NAG6 cross links two neighboring λ lysozyme molecules. Here we use NMR and MD simulations to study the interaction of λ lysozyme with the inhibitors NAG4 and NAG6 in solution. This allows us to study the interactions within the complex prior to cleavage of the polysaccharide. 1 HN and 15 N chemical shifts of λ lysozyme resonances were followed during NAG4/NAG6 titrations. The chemical shift changes were similar in the two titrations, consistent with sugars binding to the cleft between the upper and lower domains; the NMR data show no evidence for simultaneous binding of a NAG6 to two λ lysozyme molecules. Six 150 ns MD simulations of λ lysozyme in complex with NAG4 or NAG6 were performed starting from different conformations. The simulations with both NAG4 and NAG6 show stable binding of sugars across the D/E active site providing low energy models for the enzyme-inhibitor complexes. The MD simulations identify different binding subsites for the 5th and 6th sugars consistent with the NMR data. The structural information gained from the NMR experiments and MD simulations have been used to model the enzyme-peptidoglycan complex.
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Affiliation(s)
- Aysegul Turupcu
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences ViennaViennaAustria
| | | | - Alexandre Di Paolo
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des ProtéinesInstitut de Chimie, Université de LiègeLiègeBelgium
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des ProtéinesInstitut de Chimie, Université de LiègeLiègeBelgium
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences ViennaViennaAustria
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3
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Mechanism of the Escherichia coli MltE lytic transglycosylase, the cell-wall-penetrating enzyme for Type VI secretion system assembly. Sci Rep 2018. [PMID: 29515200 PMCID: PMC5841429 DOI: 10.1038/s41598-018-22527-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Lytic transglycosylases (LTs) catalyze the non-hydrolytic cleavage of the bacterial cell wall by an intramolecular transacetalization reaction. This reaction is critically and broadly important in modifications of the bacterial cell wall in the course of its biosynthesis, recycling, manifestation of virulence, insertion of structural entities such as the flagellum and the pili, among others. The first QM/MM analysis of the mechanism of reaction of an LT, that for the Escherichia coli MltE, is undertaken. The study reveals a conformational itinerary consistent with an oxocarbenium-like transition state, characterized by a pivotal role for the active-site glutamic acid in proton transfer. Notably, an oxazolinium intermediate, as a potential intermediate, is absent. Rather, substrate-assisted catalysis is observed through a favorable dipole provided by the N-acetyl carbonyl group of MurNAc saccharide. This interaction stabilizes the incipient positive charge development in the transition state. This mechanism coincides with near-synchronous acetal cleavage and acetal formation.
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4
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Williams AH, Wheeler R, Rateau L, Malosse C, Chamot-Rooke J, Haouz A, Taha MK, Boneca IG. A step-by-step in crystallo guide to bond cleavage and 1,6-anhydro-sugar product synthesis by a peptidoglycan-degrading lytic transglycosylase. J Biol Chem 2018; 293:6000-6010. [PMID: 29483188 DOI: 10.1074/jbc.ra117.001095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/12/2018] [Indexed: 01/13/2023] Open
Abstract
Lytic transglycosylases (LTs) are a class of enzymes important for the recycling and metabolism of peptidoglycan (PG). LTs cleave the β-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and GlcNAc in the PG glycan strand, resulting in the concomitant formation of 1,6-anhydro-N-acetylmuramic acid and GlcNAc. No LTs reported to date have utilized chitins as substrates, despite the fact that chitins are GlcNAc polymers linked via β-1,4-glycosidic bonds, which are the known site of chemical activity for LTs. Here, we demonstrate enzymatically that LtgA, a non-canonical, substrate-permissive LT from Neisseria meningitidis utilizes chitopentaose ((GlcNAc)5) as a substrate to produce three newly identified sugars: 1,6-anhydro-chitobiose, 1,6-anhydro-chitotriose, and 1,6-anhydro-chitotetraose. Although LTs have been widely studied, their complex reactions have not previously been visualized in the crystalline state because macromolecular PG is insoluble. Here, we visualized the cleavage of the glycosidic bond and the liberation of GlcNAc-derived residues by LtgA, followed by the synthesis of atypical 1,6-anhydro-GlcNAc derivatives. In addition to the newly identified anhydro-chitin products, we identified trapped intermediates, unpredicted substrate rearrangements, sugar distortions, and a conserved crystallographic water molecule bound to the catalytic glutamate of a high-resolution native LT. This study enabled us to propose a revised alternative mechanism for LtgA that could also be applicable to other LTs. Our work contributes to the understanding of the mechanisms of LTs in bacterial cell wall biology.
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Affiliation(s)
- Allison H Williams
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, .,INSERM, 75015 Paris, France
| | - Richard Wheeler
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France.,INSERM, 75015 Paris, France.,the Gustave Roussy Comprehensive Cancer Center, Tumour Immunology and Immunotherapy, F-94805 Villejuif, France
| | - Lesly Rateau
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France.,INSERM, 75015 Paris, France
| | - Christian Malosse
- the Institut Pasteur, CNRS USR 2000, Unité des Spectrométrie de Masse Structurale et Proteomique, 75015 Paris, France
| | - Julia Chamot-Rooke
- the Institut Pasteur, CNRS USR 2000, Unité des Spectrométrie de Masse Structurale et Proteomique, 75015 Paris, France
| | - Ahmed Haouz
- the Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR3528, 75724 Paris, France, and
| | - Muhamed-Kheir Taha
- the Institut Pasteur, Département d'Infection et Epidémiologie, Unité des Infection Bactériennes Invasives, 75015 Paris, France
| | - Ivo Gomperts Boneca
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, .,INSERM, 75015 Paris, France
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5
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Maciejewska B, Źrubek K, Espaillat A, Wiśniewska M, Rembacz KP, Cava F, Dubin G, Drulis-Kawa Z. Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue. Sci Rep 2017; 7:14501. [PMID: 29109551 PMCID: PMC5674055 DOI: 10.1038/s41598-017-14797-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/16/2017] [Indexed: 01/19/2023] Open
Abstract
Endolysins are peptidoglycan-degrading enzymes utilized by bacteriophages to release the progeny from bacterial cells. The lytic properties of phage endolysins make them potential antibacterial agents for medical and industrial applications. Here, we present a comprehensive characterization of phage AP3 modular endolysin (AP3gp15) containing cell wall binding domain and an enzymatic domain (DUF3380 by BLASTP), both widespread and conservative. Our structural analysis demonstrates the low similarity of an enzymatic domain to known lysozymes and an unusual catalytic centre characterized by only a single glutamic acid residue and no aspartic acid. Thus, our findings suggest distinguishing a novel class of muralytic enzymes having the activity and catalytic centre organization of DUF3380. The lack of amino acid sequence homology between AP3gp15 and other known muralytic enzymes may reflect the evolutionary convergence of analogous glycosidases. Moreover, the broad antibacterial spectrum, lack of cytotoxic effect on human cells and the stability characteristics of AP3 endolysin advocate for its future application development.
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Affiliation(s)
- Barbara Maciejewska
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Karol Źrubek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine Sweden. Molecular Biology Department, Umeå University, SE-901 87, Umeå, Sweden
| | - Magdalena Wiśniewska
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Krzysztof P Rembacz
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden. Molecular Biology Department, Umeå University, SE-901 87, Umeå, Sweden
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland.
| | - Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
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6
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Dik DA, Marous DR, Fisher JF, Mobashery S. Lytic transglycosylases: concinnity in concision of the bacterial cell wall. Crit Rev Biochem Mol Biol 2017. [PMID: 28644060 DOI: 10.1080/10409238.2017.1337705] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores. Significant advances in the mechanistic understanding of each of these processes have coincided with the successive discovery of new LTs structures. In this review, we provide a systematic perspective on what is known on the structure-function correlations for the LTs, while simultaneously identifying numerous opportunities for the future study of these enigmatic enzymes.
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Affiliation(s)
- David A Dik
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Daniel R Marous
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Jed F Fisher
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Shahriar Mobashery
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
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7
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Pseudomonas aeruginosa: targeting cell-wall metabolism for new antibacterial discovery and development. Future Med Chem 2016; 8:975-92. [PMID: 27228070 DOI: 10.4155/fmc-2016-0017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas aeruginosa is a leading cause of hospital-acquired infections and is resistant to most antibiotics. With therapeutic options against P. aeruginosa dwindling, and the lack of new antibiotics in advanced developmental stages, strategies for preserving the effectiveness of current antibiotics are urgently required. β-Lactam antibiotics are important agents for treating P. aeruginosa infections, thus, adjuvants that potentiate the activity of these compounds are desirable for extending their lifespan while new antibiotics - or antibiotic classes - are discovered and developed. In this review, we discuss recent research that has identified exploitable targets of cell-wall metabolism for the design and development of compounds that hinder resistance and potentiate the activity of antipseudomonal β-lactams.
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8
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Vaughan MD, Su Z, Daub E, Honek JF. Intriguing cellular processing of a fluorinated amino acid during protein biosynthesis in Escherichia coli. Org Biomol Chem 2016; 14:8942-8946. [DOI: 10.1039/c6ob01690a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unusual in vivo processing of a fluorinated amino acid provides unexpected dual protein labeling in E. coli.
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Affiliation(s)
- Mark D. Vaughan
- Department of Chemistry
- University of Waterloo
- Waterloo
- ON N2L 3G1 Canada
| | - Zhengding Su
- Department of Chemistry
- University of Waterloo
- Waterloo
- ON N2L 3G1 Canada
| | - Elisabeth Daub
- Department of Chemistry
- University of Waterloo
- Waterloo
- ON N2L 3G1 Canada
| | - J. F. Honek
- Department of Chemistry
- University of Waterloo
- Waterloo
- ON N2L 3G1 Canada
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9
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Herlihey FA, Clarke AJ. Controlling Autolysis During Flagella Insertion in Gram-Negative Bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:41-56. [PMID: 27722959 DOI: 10.1007/5584_2016_52] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The flagellum is an important macromolecular machine for many pathogenic bacteria. It is a hetero-oligomeric structure comprised of three major sub-structures: basal body, hook and thin helical filament. An important step during flagellum assembly is the localized and controlled degradation of the peptidoglycan sacculus to allow for the insertion of the rod as well as to facilitate anchoring for proper motor function. The peptidoglycan lysis events require specialized lytic enzymes, β-N-acetylglucosaminidases and lytic transglycosylases, which differ in flagellated proteobacteria. Due to their autolytic activity, these enzymes need to be controlled in order to prevent cellular lysis. This review summarizes are current understanding of the peptidoglycan lysis events required for flagellum assembly and motility with a main focus on Gram-negative bacteria.
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Affiliation(s)
- Francesca A Herlihey
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada.
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10
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Smith LJ, van Gunsteren WF, Hansen N. Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:235-47. [DOI: 10.1007/s00249-015-1018-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/27/2015] [Accepted: 03/05/2015] [Indexed: 12/27/2022]
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11
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TraG encoded by the pIP501 type IV secretion system is a two-domain peptidoglycan-degrading enzyme essential for conjugative transfer. J Bacteriol 2013; 195:4436-44. [PMID: 23913323 DOI: 10.1128/jb.02263-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
pIP501 is a conjugative broad-host-range plasmid frequently present in nosocomial Enterococcus faecalis and Enterococcus faecium isolates. We focus here on the functional analysis of the type IV secretion gene traG, which was found to be essential for pIP501 conjugative transfer between Gram-positive bacteria. The TraG protein, which localizes to the cell envelope of E. faecalis harboring pIP501, was expressed and purified without its N-terminal transmembrane helix (TraGΔTMH) and shown to possess peptidoglycan-degrading activity. TraGΔTMH was inhibited by specific lytic transglycosylase inhibitors hexa-N-acetylchitohexaose and bulgecin A. Analysis of the TraG sequence suggested the presence of two domains which both could contribute to the observed cell wall-degrading activity: an N-terminal soluble lytic transglycosylase domain (SLT) and a C-terminal cysteine-, histidine-dependent amidohydrolases/peptidases (CHAP) domain. The protein domains were expressed separately, and both degraded peptidoglycan. A change of the conserved glutamate residue in the putative catalytic center of the SLT domain (E87) to glycine resulted in almost complete inactivity, which is consistent with this part of TraG being a predicted lytic transglycosylase. Based on our findings, we propose that TraG locally opens the peptidoglycan to facilitate insertion of the Gram-positive bacterial type IV secretion machinery into the cell envelope.
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12
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Smith LJ, Bowen AM, Di Paolo A, Matagne A, Redfield C. The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations. Chembiochem 2013; 14:1780-8. [DOI: 10.1002/cbic.201300193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 11/09/2022]
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13
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Zeng X, Lin J. Beta-lactamase induction and cell wall metabolism in Gram-negative bacteria. Front Microbiol 2013; 4:128. [PMID: 23734147 PMCID: PMC3660660 DOI: 10.3389/fmicb.2013.00128] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/04/2013] [Indexed: 11/13/2022] Open
Abstract
Production of beta-lactamases, the enzymes that degrade beta-lactam antibiotics, is the most widespread and threatening mechanism of antibiotic resistance. In the past, extensive research has focused on the structure, function, and ecology of beta-lactamases while limited efforts were placed on the regulatory mechanisms of beta-lactamases. Recently, increasing evidence demonstrate a direct link between beta-lactamase induction and cell wall metabolism in Gram-negative bacteria. Specifically, expression of beta-lactamase could be induced by the liberated murein fragments, such as muropeptides. This article summarizes current knowledge on cell wall metabolism, beta-lactam antibiotics, and beta-lactamases. In particular, we comprehensively reviewed recent studies on the beta-lactamase induction by muropeptides via two major molecular mechanisms (the AmpG-AmpR-AmpC pathway and BlrAB-like two-component regulatory system) in Gram-negative bacteria. The signaling pathways for beta-lactamase induction offer a broad array of promising targets for the discovery of new antibacterial drugs used for combination therapies. Therefore, to develop effective mitigation strategies against the widespread beta-lactam resistance, examination of the molecular basis of beta-lactamase induction by cell wall fragment is highly warranted.
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Affiliation(s)
| | - Jun Lin
- Department of Animal Science, The University of TennesseeKnoxville, TN, USA
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14
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Schmelcher M, Donovan DM, Loessner MJ. Bacteriophage endolysins as novel antimicrobials. Future Microbiol 2013; 7:1147-71. [PMID: 23030422 DOI: 10.2217/fmb.12.97] [Citation(s) in RCA: 490] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endolysins are enzymes used by bacteriophages at the end of their replication cycle to degrade the peptidoglycan of the bacterial host from within, resulting in cell lysis and release of progeny virions. Due to the absence of an outer membrane in the Gram-positive bacterial cell wall, endolysins can access the peptidoglycan and destroy these organisms when applied externally, making them interesting antimicrobial candidates, particularly in light of increasing bacterial drug resistance. This article reviews the modular structure of these enzymes, in which cell wall binding and catalytic functions are separated, as well as their mechanism of action, lytic activity and potential as antimicrobials. It particularly focuses on molecular engineering as a means of optimizing endolysins for specific applications, highlights new developments that may render these proteins active against Gram-negative and intracellular pathogens and summarizes the most recent applications of endolysins in the fields of medicine, food safety, agriculture and biotechnology.
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Affiliation(s)
- Mathias Schmelcher
- Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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15
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Dessau M, Goldhill D, McBride RL, Turner PE, Modis Y. Selective pressure causes an RNA virus to trade reproductive fitness for increased structural and thermal stability of a viral enzyme. PLoS Genet 2012; 8:e1003102. [PMID: 23209446 PMCID: PMC3510033 DOI: 10.1371/journal.pgen.1003102] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 10/03/2012] [Indexed: 11/18/2022] Open
Abstract
The modulation of fitness by single mutational substitutions during environmental change is the most fundamental consequence of natural selection. The antagonistic tradeoffs of pleiotropic mutations that can be selected under changing environments therefore lie at the foundation of evolutionary biology. However, the molecular basis of fitness tradeoffs is rarely determined in terms of how these pleiotropic mutations affect protein structure. Here we use an interdisciplinary approach to study how antagonistic pleiotropy and protein function dictate a fitness tradeoff. We challenged populations of an RNA virus, bacteriophage Φ6, to evolve in a novel temperature environment where heat shock imposed extreme virus mortality. A single amino acid substitution in the viral lysin protein P5 (V207F) favored improved stability, and hence survival of challenged viruses, despite a concomitant tradeoff that decreased viral reproduction. This mutation increased the thermostability of P5. Crystal structures of wild-type, mutant, and ligand-bound P5 reveal the molecular basis of this thermostabilization--the Phe207 side chain fills a hydrophobic cavity that is unoccupied in the wild-type--and identify P5 as a lytic transglycosylase. The mutation did not reduce the enzymatic activity of P5, suggesting that the reproduction tradeoff stems from other factors such as inefficient capsid assembly or disassembly. Our study demonstrates how combining experimental evolution, biochemistry, and structural biology can identify the mechanisms that drive the antagonistic pleiotropic phenotypes of an individual point mutation in the classic evolutionary tug-of-war between survival and reproduction.
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Affiliation(s)
- Moshe Dessau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Daniel Goldhill
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Robert L. McBride
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Yorgo Modis
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
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16
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Walmagh M, Boczkowska B, Grymonprez B, Briers Y, Drulis-Kawa Z, Lavigne R. Characterization of five novel endolysins from Gram-negative infecting bacteriophages. Appl Microbiol Biotechnol 2012; 97:4369-75. [DOI: 10.1007/s00253-012-4294-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 11/30/2022]
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17
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Pham E, Truong K. Engineered regulation of lysozyme by the SH3-CB1 binding interaction. Protein Eng Des Sel 2012; 25:307-11. [PMID: 22532698 DOI: 10.1093/protein/gzs020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The ability to design proteins with desired properties by using protein structural information will allow us to create high-value therapeutic and diagnostic products. Using the protein structures of lambda lysozyme and the SH3 domain of human Crk, we designed a synthetic protein switch that controls the activity of lysozyme by sterically hindering its active cleft through the binding of SH3 to its CB1 peptide-binding partner. First, several fusion protein designs with lysozyme and CB1 were modeled to determine the one with greatest steric effect in the presence of SH3. Next, the selected fusion protein was created and tested in vitro. In the absence of SH3, the lysozyme-CB1 fusion protein functioned normally. In the presence of SH3, the lysozyme activity was inhibited and with the addition of excess CB1 peptides to compete for SH3 binding, the lysozyme activity was restored. Lastly, this structure-based strategy can be used to engineer synthetic regulation by peptide-domain-binding interfaces into a variety of proteins.
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Affiliation(s)
- Elizabeth Pham
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
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Chertkov OV, Chuprov-Netochin RN, Legotskiĭ SV, Sykilinda NN, Shneider MM, Ivanova MA, Pleteneva EA, Shaburova OV, Burkal'tseva MB, Kostriukova ES, Lazarev VN, Kliachko NL, Miroshnikov KA. Properties of the peptidoglycan-degrading enzyme of the Pseudomonas aeruginosa ϕPMG1 bacteriophage. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:807-14. [PMID: 22497079 DOI: 10.1134/s1068162011060057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rajagopala SV, Casjens S, Uetz P. The protein interaction map of bacteriophage lambda. BMC Microbiol 2011; 11:213. [PMID: 21943085 PMCID: PMC3224144 DOI: 10.1186/1471-2180-11-213] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 09/26/2011] [Indexed: 11/25/2022] Open
Abstract
Background Bacteriophage lambda is a model phage for most other dsDNA phages and has been studied for over 60 years. Although it is probably the best-characterized phage there are still about 20 poorly understood open reading frames in its 48-kb genome. For a complete understanding we need to know all interactions among its proteins. We have manually curated the lambda literature and compiled a total of 33 interactions that have been found among lambda proteins. We set out to find out how many protein-protein interactions remain to be found in this phage. Results In order to map lambda's interactions, we have cloned 68 out of 73 lambda open reading frames (the "ORFeome") into Gateway vectors and systematically tested all proteins for interactions using exhaustive array-based yeast two-hybrid screens. These screens identified 97 interactions. We found 16 out of 30 previously published interactions (53%). We have also found at least 18 new plausible interactions among functionally related proteins. All previously found and new interactions are combined into structural and network models of phage lambda. Conclusions Phage lambda serves as a benchmark for future studies of protein interactions among phage, viruses in general, or large protein assemblies. We conclude that we could not find all the known interactions because they require chaperones, post-translational modifications, or multiple proteins for their interactions. The lambda protein network connects 12 proteins of unknown function with well characterized proteins, which should shed light on the functional associations of these uncharacterized proteins.
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Wohlkönig A, Huet J, Looze Y, Wintjens R. Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs. PLoS One 2010; 5:e15388. [PMID: 21085702 PMCID: PMC2976769 DOI: 10.1371/journal.pone.0015388] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 08/31/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Chitin is a polysaccharide that forms the hard, outer shell of arthropods and the cell walls of fungi and some algae. Peptidoglycan is a polymer of sugars and amino acids constituting the cell walls of most bacteria. Enzymes that are able to hydrolyze these cell membrane polymers generally play important roles for protecting plants and animals against infection with insects and pathogens. A particular group of such glycoside hydrolase enzymes share some common features in their three-dimensional structure and in their molecular mechanism, forming the lysozyme superfamily. RESULTS Besides having a similar fold, all known catalytic domains of glycoside hydrolase proteins of lysozyme superfamily (families and subfamilies GH19, GH22, GH23, GH24 and GH46) share in common two structural elements: the central helix of the all-α domain, which invariably contains the catalytic glutamate residue acting as general-acid catalyst, and a β-hairpin pointed towards the substrate binding cleft. The invariant β-hairpin structure is interestingly found to display the highest amino acid conservation in aligned sequences of a given family, thereby allowing to define signature motifs for each GH family. Most of such signature motifs are found to have promising performances for searching sequence databases. Our structural analysis further indicates that the GH motifs participate in enzymatic catalysis essentially by containing the catalytic water positioning residue of inverting mechanism. CONCLUSIONS The seven families and subfamilies of the lysozyme superfamily all have in common a β-hairpin structure which displays a family-specific sequence motif. These GH β-hairpin motifs contain potentially important residues for the catalytic activity, thereby suggesting the participation of the GH motif to catalysis and also revealing a common catalytic scheme utilized by enzymes of the lysozyme superfamily.
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Affiliation(s)
- Alexandre Wohlkönig
- Structural Biology Brussels and Molecular and Cellular Interactions, VIB, Brussels, Belgium
| | - Joëlle Huet
- Laboratoire de Chimie Générale, Institut de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Yvan Looze
- Laboratoire de Chimie Générale, Institut de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - René Wintjens
- Laboratoire de Chimie Générale, Institut de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
- Interdisciplinary Research Institute, USR 3078 CNRS, Villeneuve d'Ascq, France
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Di Paolo A, Balbeur D, De Pauw E, Redfield C, Matagne A. Rapid collapse into a molten globule is followed by simple two-state kinetics in the folding of lysozyme from bacteriophage λ. Biochemistry 2010; 49:8646-57. [PMID: 20806781 DOI: 10.1021/bi101126f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stopped-flow fluorescence and circular dichroism spectroscopy have been used in combination with quenched-flow hydrogen exchange labeling, monitored by two-dimensional NMR and electrospray ionization mass spectrometry, to investigate the folding kinetics of lysozyme from bacteriophage λ (λ lysozyme) at pH 5.6, 20 °C. The first step in the folding of λ lysozyme occurs very rapidly (τ < 1 ms) after refolding is initiated and involves both hydrophobic collapse and formation of a high content of secondary structure but only weak protection from (1)H/(2)H exchange and no fixed tertiary structure organization. This early folding step is reflected in the dead-time events observed in the far-UV CD and ANS fluorescence experiments. Following accumulation of this kinetic molten globule species, the secondary structural elements are stabilized and the majority (ca. 88%) of refolding molecules acquire native-like properties in a highly cooperative two-state process, with τ = 0.15 ± 0.03 s. This is accompanied by the acquisition of substantial native-like protection from hydrogen exchange. A double-mixing experiment and the absence of a denaturant effect reveal that slow (τ = 5 ± 1 s) folding of the remaining (ca. 12%) molecules is rate limited by the cis/trans isomerization of prolines that are trans in the folded enzyme. In addition, native state hydrogen exchange and classical denaturant unfolding experiments have been used to characterize the thermodynamic properties of the enzyme. In good agreement with previous crystallographic evidence, our results show that λ lysozyme is a highly dynamic protein, with relatively low conformational stability (ΔG°(N-U) = 25 ± 2 kJ·mol(-1)).
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Affiliation(s)
- Alexandre Di Paolo
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
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22
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Di Paolo A, Duval V, Matagne A, Redfield C. Backbone 1H, 13C, and 15N resonance assignments for lysozyme from bacteriophage lambda. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:111-114. [PMID: 20300891 PMCID: PMC2862172 DOI: 10.1007/s12104-010-9219-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/02/2010] [Indexed: 05/29/2023]
Abstract
Lysozyme from lambda bacteriophage (lambda lysozyme) is an 18 kDa globular protein displaying some of the structural features common to all lysozymes; in particular, lambda lysozyme consists of two structural domains connected by a helix, and has its catalytic residues located at the interface between these two domains. An interesting feature of lambda lysozyme, when compared to the well-characterised hen egg-white lysozyme, is its lack of disulfide bridges; this makes lambda lysozyme an interesting system for studies of protein folding. A comparison of the folding properties of lambda lysozyme and hen lysozyme will provide important insights into the role that disulfide bonds play in the refolding pathway of the latter protein. Here we report the (1)H, (13)C and (15)N backbone resonance assignments for lambda lysozyme by heteronuclear multidimensional NMR spectroscopy. These assignments provide the starting point for detailed investigation of the refolding pathway using pulse-labelling hydrogen/deuterium exchange experiments monitored by NMR.
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Affiliation(s)
- Alexandre Di Paolo
- Laboratoire d’Enzymologie et Repliement des protéines, Centre d’Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B4000 Liège (Sart-Tilman), Belgium
| | - Valérie Duval
- Laboratoire d’Enzymologie et Repliement des protéines, Centre d’Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B4000 Liège (Sart-Tilman), Belgium
| | - André Matagne
- Laboratoire d’Enzymologie et Repliement des protéines, Centre d’Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B4000 Liège (Sart-Tilman), Belgium
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU United Kingdom
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. COMPREHENSIVE NATURAL PRODUCTS II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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24
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Crystal Structure of the Resuscitation-Promoting Factor ΔDUFRpfB from M. tuberculosis. J Mol Biol 2009; 385:153-62. [DOI: 10.1016/j.jmb.2008.10.042] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 09/29/2008] [Accepted: 10/08/2008] [Indexed: 11/23/2022]
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25
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Structural details of the glycosyltransferase step of peptidoglycan assembly. Curr Opin Struct Biol 2008; 18:534-43. [DOI: 10.1016/j.sbi.2008.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 07/06/2008] [Accepted: 07/22/2008] [Indexed: 11/21/2022]
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26
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Vollmer W, Joris B, Charlier P, Foster S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol Rev 2008; 32:259-86. [PMID: 18266855 DOI: 10.1111/j.1574-6976.2007.00099.x] [Citation(s) in RCA: 609] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Most bacteria have multiple peptidoglycan hydrolases capable of cleaving covalent bonds in peptidoglycan sacculi or its fragments. An overview of the different classes of peptidoglycan hydrolases and their cleavage sites is provided. The physiological functions of these enzymes include the regulation of cell wall growth, the turnover of peptidoglycan during growth, the separation of daughter cells during cell division and autolysis. Specialized hydrolases enlarge the pores in the peptidoglycan for the assembly of large trans-envelope complexes (pili, flagella, secretion systems), or they specifically cleave peptidoglycan during sporulation or spore germination. Moreover, peptidoglycan hydrolases are involved in lysis phenomena such as fratricide or developmental lysis occurring in bacterial populations. We will also review the current view on the regulation of autolysins and on the role of cytoplasm hydrolases in peptidoglycan recycling and induction of beta-lactamase.
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Affiliation(s)
- Waldemar Vollmer
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne, UK.
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27
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Scheurwater E, Reid CW, Clarke AJ. Lytic transglycosylases: Bacterial space-making autolysins. Int J Biochem Cell Biol 2008; 40:586-91. [PMID: 17468031 DOI: 10.1016/j.biocel.2007.03.018] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 03/20/2007] [Accepted: 03/21/2007] [Indexed: 11/29/2022]
Abstract
Lytic transglycosylases are an important class of bacterial enzymes that act on peptidoglycan with the same substrate specificity as lysozyme. Unlike the latter enzymes, however, the lytic transglycosylases are not hydrolases but instead cleave the glycosidic linkage between N-actetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anydromuramoyl product. They are ubiquitous in bacteria which produce a compliment of different forms that are responsible for creating space within the peptidoglycan sacculus for its biosynthesis and recycling, cell division, and the insertion of cell-envelope spanning structures, such as flagella and secretion systems. As well, the lytic transglyosylases may have a role in pathogenesis of some bacterial species. Given their important role in bacterial cell wall metabolism, the lytic transglycosylases may present an attractive new target for the development of broad-spectrum antibiotics.
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Affiliation(s)
- Edie Scheurwater
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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28
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Lovering AL, de Castro LH, Lim D, Strynadka NCJ. Structural Insight into the Transglycosylation Step of Bacterial Cell-Wall Biosynthesis. Science 2007; 315:1402-5. [PMID: 17347437 DOI: 10.1126/science.1136611] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Peptidoglycan glycosyltransferases (GTs) catalyze the polymerization step of cell-wall biosynthesis, are membrane-bound, and are highly conserved across all bacteria. Long considered the "holy grail" of antibiotic research, they represent an essential and easily accessible drug target for antibiotic-resistant bacteria, including methicillin-resistant Staphylococcus aureus. We have determined the 2.8 angstrom structure of a bifunctional cell-wall cross-linking enzyme, including its transpeptidase and GT domains, both unliganded and complexed with the substrate analog moenomycin. The peptidoglycan GTs adopt a fold distinct from those of other GT classes. The structures give insight into critical features of the catalytic mechanism and key interactions required for enzyme inhibition.
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Affiliation(s)
- Andrew L Lovering
- Department of Biochemistry and Molecular Biology, and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada
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29
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Yuan Y, Barrett D, Zhang Y, Kahne D, Sliz P, Walker S. Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis. Proc Natl Acad Sci U S A 2007; 104:5348-53. [PMID: 17360321 PMCID: PMC1817829 DOI: 10.1073/pnas.0701160104] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peptidoglycan is an essential polymer that forms a protective shell around bacterial cell membranes. Peptidoglycan biosynthesis is the target of many clinically used antibiotics, including the beta-lactams, imipenems, cephalosporins, and glycopeptides. Resistance to these and other antibiotics has prompted interest in an atomic-level understanding of the enzymes that make peptidoglycan. Representative structures have been reported for most of the enzymes in the pathway. Until now, however, there have been no structures of any peptidoglycan glycosyltransferases (also known as transglycosylases), which catalyze formation of the carbohydrate chains of peptidoglycan from disaccharide subunits on the bacterial cell surface. We report here the 2.1-A crystal structure of the peptidoglycan glycosyltransferase (PGT) domain of Aquifex aeolicus PBP1A. The structure has a different fold from all other glycosyltransferase structures reported to date, but it bears some resemblance to lambda-lysozyme, an enzyme that degrades the carbohydrate chains of peptidoglycan. An analysis of the structure, combined with biochemical information showing that these enzymes are processive, suggests a model for glycan chain polymerization.
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Affiliation(s)
- Yanqiu Yuan
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
| | - Dianah Barrett
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
| | - Yi Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; and
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; and
- To whom correspondence may be addressed. E-mail: or
| | - Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
- To whom correspondence may be addressed. E-mail: or
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30
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Zhou Y, Yang W, Kirberger M, Lee HW, Ayalasomayajula G, Yang JJ. Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins. Proteins 2007; 65:643-55. [PMID: 16981205 DOI: 10.1002/prot.21139] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The EF-hand protein with a helix-loop-helix Ca(2+) binding motif constitutes one of the largest protein families and is involved in numerous biological processes. To facilitate the understanding of the role of Ca(2+) in biological systems using genomic information, we report, herein, our improvement on the pattern search method for the identification of EF-hand and EF-like Ca(2+)-binding proteins. The canonical EF-hand patterns are modified to cater to different flanking structural elements. In addition, on the basis of the conserved sequence of both the N- and C-terminal EF-hands within S100 and S100-like proteins, a new signature profile has been established to allow for the identification of pseudo EF-hand and S100 proteins from genomic information. The new patterns have a positive predictive value of 99% and a sensitivity of 96% for pseudo EF-hands. Furthermore, using the developed patterns, we have identified zero pseudo EF-hand motif and 467 canonical EF-hand Ca(2+) binding motifs with diverse cellular functions in the bacteria genome. The prediction results imply that pseudo EF-hand motifs are phylogenetically younger than canonical EF-hand motifs. Our prediction of Ca(2+) binding motifs provides not only an insight into the role of Ca(2+) and Ca(2+)-binding proteins in bacterial systems, but also a way to explore and define the role of Ca(2+) in other biological systems (calciomics).
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Affiliation(s)
- Yubin Zhou
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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31
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Sreekanth R, Rajan SS. The study of helical distortions due to environmental changes: choice of parameters. Biophys Chem 2007; 125:191-200. [PMID: 16919383 DOI: 10.1016/j.bpc.2006.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 07/28/2006] [Accepted: 07/29/2006] [Indexed: 10/24/2022]
Abstract
Parameters like interhelical angles, helical parameters, levels of distortions, etc., have been analysed to test their sensitivity to environmental changes using a method developed in this laboratory. This analysis was done on protein structures solved under different environmental conditions like temperature and pH, and ligand binding. The study reveals that the helical parameters are not sensitive enough to study the effect of environmental changes on protein helices. On the other hand the helical distortions as well as changes in the interhelical angles are more sensitive to these changes. The study also provides with additional information like the origin of distortions in a helix when a ligand binds to a protein, bending in helical axis, identification and extent of domain movements, etc.
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Affiliation(s)
- R Sreekanth
- Deparment of Crystallography and Biophysics, University of Madras, Chennai, India
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32
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Kohler PL, Cloud KA, Hackett KT, Beck ET, Dillard JP. Characterization of the role of LtgB, a putative lytic transglycosylase in Neisseria gonorrhoeae. MICROBIOLOGY-SGM 2005; 151:3081-3088. [PMID: 16151218 DOI: 10.1099/mic.0.28125-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Neisseria gonorrhoeae releases monomeric peptidoglycan (PG) fragments during growth. These PG fragments affect pathogenesis-related phenotypes including induction of inflammatory cytokines and killing of ciliated fallopian tube cells. Although the biological activities of these molecules have been established in multiple systems, the genes and gene products responsible for their production in N. gonorrhoeae have not been determined. The authors previously identified genes for three lytic transglycosylase homologues (ltgA, ltgB and ltgC) in the N. gonorrhoeae genome sequence. Mutation of ltgA was found to affect PG fragment release, and mutation of ltgC affected cell separation. In this study the effects of complete deletion or point mutations in ltgB were characterized. Point mutations were introduced by a combination of insertion-duplication mutagenesis and positive and negative selection, thereby generating selectable marker-less mutations. The ltgB deletion mutant had normal growth characteristics and was not affected in PG fragment release. When expressed in Escherichia coli, gonococcal LtgB was able to substitute for lambda endolysin to cause cell lysis. Mutation of the predicted catalytic-site glutamic acid residue did not decrease lysis in this system. However, mutation of a nearby glutamic acid residue eliminated lysis activity.
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Affiliation(s)
- Petra L Kohler
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Medical School, Madison, 1300 University Avenue, 471A MSC, WI 53706, USA
| | - Karen A Cloud
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Medical School, Madison, 1300 University Avenue, 471A MSC, WI 53706, USA
| | - Kathleen T Hackett
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Medical School, Madison, 1300 University Avenue, 471A MSC, WI 53706, USA
| | - Eric T Beck
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Medical School, Madison, 1300 University Avenue, 471A MSC, WI 53706, USA
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Medical School, Madison, 1300 University Avenue, 471A MSC, WI 53706, USA
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Höppner C, Carle A, Sivanesan D, Hoeppner S, Baron C. The putative lytic transglycosylase VirB1 from Brucella suis interacts with the type IV secretion system core components VirB8, VirB9 and VirB11. MICROBIOLOGY-SGM 2005; 151:3469-3482. [PMID: 16272371 DOI: 10.1099/mic.0.28326-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
VirB1-like proteins are believed to act as lytic transglycosylases, which facilitate the assembly of type IV secretion systems via localized lysis of the peptidoglycan. This paper presents the biochemical analysis of interactions of purified Brucella suis VirB1 with core components of the type IV secretion system. Genes encoding VirB1, VirB8, VirB9, VirB10 and VirB11 were cloned into expression vectors; the affinity-tagged proteins were purified from Escherichia coli, and analyses by gel filtration chromatography showed that they form monomers or homo-multimers. Analysis of protein-protein interactions by affinity precipitation revealed that VirB1 bound to VirB9 and VirB11. The results of bicistron expression experiments followed by gel filtration further supported the VirB1-VirB9 interaction. Peptide array mapping identified regions of VirB1 that interact with VirB8, VirB9 and VirB11 and underscored the importance of the C-terminus, especially for the VirB1-VirB9 interaction. The binding sites were localized on a structure model of VirB1, suggesting that different portions of VirB1 may interact with other VirB proteins during assembly of the type IV secretion machinery.
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Affiliation(s)
- Christoph Höppner
- Ludwig-Maximilians-Universität, Department Biologie I, Bereich Mikrobiologie, Maria-Ward-Str. 1a, D-80638 München, Germany
| | - Anna Carle
- Ludwig-Maximilians-Universität, Department Biologie I, Bereich Mikrobiologie, Maria-Ward-Str. 1a, D-80638 München, Germany
| | - Durga Sivanesan
- McMaster University, Department of Biology, 1280 Main St West, Hamilton, ON, Canada LS8 4K1
| | - Sabine Hoeppner
- Ludwig-Maximilians-Universität, Gene Center, Feodor-Lynen Str. 25, D-81377 München, Germany
| | - Christian Baron
- McMaster University, Department of Biology, 1280 Main St West, Hamilton, ON, Canada LS8 4K1
- Ludwig-Maximilians-Universität, Department Biologie I, Bereich Mikrobiologie, Maria-Ward-Str. 1a, D-80638 München, Germany
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Zahrl D, Wagner M, Bischof K, Bayer M, Zavecz B, Beranek A, Ruckenstuhl C, Zarfel GE, Koraimann G. Peptidoglycan degradation by specialized lytic transglycosylases associated with type III and type IV secretion systems. Microbiology (Reading) 2005; 151:3455-3467. [PMID: 16272370 DOI: 10.1099/mic.0.28141-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Specialized lytic transglycosylases are muramidases capable of locally degrading the peptidoglycan meshwork of Gram-negative bacteria. Specialized lytic transglycosylase genes are present in clusters encoding diverse macromolecular transport systems. This paper reports the analysis of selected members of the specialized lytic transglycosylase family from type III and type IV secretion systems. These proteins were analysedin vivoby assaying their ability to complement the DNA transfer defect of the conjugative F-like plasmid R1-16 lacking a functional P19 protein, the specialized lytic transglycosylase of this type IV secretion system. Heterologous complementation was accomplished using IpgF from the plasmid-encoded type III secretion system ofShigella sonneiand TrbN from the type IV secretion system of the conjugative plasmid RP4. In contrast, neither VirB1 proteins (Agrobacterium tumefaciens,Brucella suis) nor IagB (Salmonella enterica) could functionally replace P19.In vitro, IpgF, IagB, both VirB1 proteins, HP0523 (Helicobacter pylori) and P19 displayed peptidoglycanase activity in zymogram analyses. Using an established test system and a newly developed assay it was shown that IpgF degraded peptidoglycan in solution. IpgF was active only after removal of the chaperonin GroEL, which co-purified with IpgF and inhibited its enzymic activity. A mutant IpgF protein in which the predicted catalytic amino acid, Glu42, was replaced by Gln, was completely inactive. IpgF-catalysed peptidoglycan degradation was optimal at pH 6 and was inhibited by the lytic transglycosylase inhibitors hexa-N-acetylchitohexaose and bulgecin A.
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Affiliation(s)
- Doris Zahrl
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Maria Wagner
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Karin Bischof
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Michaela Bayer
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Barbara Zavecz
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Andreas Beranek
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Christoph Ruckenstuhl
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Gernot E Zarfel
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Günther Koraimann
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
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35
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Loessner MJ. Bacteriophage endolysins--current state of research and applications. Curr Opin Microbiol 2005; 8:480-7. [PMID: 15979390 DOI: 10.1016/j.mib.2005.06.002] [Citation(s) in RCA: 368] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 06/09/2005] [Indexed: 11/27/2022]
Abstract
Endolysins are phage-encoded enzymes that break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. Their action is tightly regulated by holins, by membrane arrest, and by conversion from their inactive to active state. Recent research has not only revealed the unexpected diversity of these highly specific hydrolases but has also yielded insights into their modular organization and their three-dimensional structures. Their N-terminal catalytic domains are able to target almost every possible bond in the peptidoglycan network, and their corresponding C-terminal cell wall binding domains target the enzymes to their substrate. Owing to their specificity and high activity, endolysins have been employed for various in vitro and in vivo aims, in food science, in microbial diagnostics, and for treatment of experimental infections. Clearly, phage endolysins represent great tools for use in molecular biology, biotechnology and in medicine, and we are just beginning to tap this potential.
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Affiliation(s)
- Martin J Loessner
- Institute of Food Science and Nutrition, Swiss Federal Institute of Technology (ETH), Schmelzbergstrasse 7, CH-8092 Zürich, Switzerland.
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36
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van Straaten KE, Dijkstra BW, Vollmer W, Thunnissen AMWH. Crystal Structure of MltA from Escherichia coli Reveals a Unique Lytic Transglycosylase Fold. J Mol Biol 2005; 352:1068-80. [PMID: 16139297 DOI: 10.1016/j.jmb.2005.07.067] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2005] [Revised: 07/21/2005] [Accepted: 07/26/2005] [Indexed: 10/25/2022]
Abstract
Lytic transglycosylases are bacterial enzymes involved in the maintenance and growth of the bacterial cell-wall peptidoglycan. They cleave the beta-(1,4)-glycosidic bonds in peptidoglycan forming non-reducing 1,6-anhydromuropeptides. The crystal structure of the lytic transglycosylase MltA from Escherichia coli without a membrane anchor was solved at 2.0A resolution. The enzyme has a fold completely different from those of the other known lytic transglycosylases. It contains two domains, the largest of which has a double-psi beta-barrel fold, similar to that of endoglucanase V from Humicola insolens. The smaller domain also has a beta-barrel fold topology, which is weakly related to that of the RNA-binding domain of ribosomal proteins L25 and TL5. A large groove separates the two domains, which can accommodate a glycan strand, as shown by molecular modelling. Several conserved residues, one of which is in a position equivalent to that of the catalytic acid of the H.insolens endoglucanase, flank this putative substrate-binding groove. Mutation of this residue, Asp308, abolished all activity of the enzyme, supporting the direct participation of this residue in catalysis.
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Affiliation(s)
- Karin E van Straaten
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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