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Hsu TW, Fang JM. Advances and prospects of analytic methods for bacterial transglycosylation and inhibitor discovery. Analyst 2024; 149:2204-2222. [PMID: 38517346 DOI: 10.1039/d3an01968c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The cell wall is essential for bacteria to maintain structural rigidity and withstand external osmotic pressure. In bacteria, the cell wall is composed of peptidoglycan. Lipid II is the basic unit for constructing highly cross-linked peptidoglycan scaffolds. Transglycosylase (TGase) is the initiating enzyme in peptidoglycan synthesis that catalyzes the ligation of lipid II moieties into repeating GlcNAc-MurNAc polysaccharides, followed by transpeptidation to generate cross-linked structures. In addition to the transglycosylases in the class-A penicillin-binding proteins (aPBPs), SEDS (shape, elongation, division and sporulation) proteins are also present in most bacteria and play vital roles in cell wall renewal, elongation, and division. In this review, we focus on the latest analytical methods including the use of radioactive labeling, gel electrophoresis, mass spectrometry, fluorescence labeling, probing undecaprenyl pyrophosphate, fluorescence anisotropy, ligand-binding-induced tryptophan fluorescence quenching, and surface plasmon resonance to evaluate TGase activity in cell wall formation. This review also covers the discovery of TGase inhibitors as potential antibacterial agents. We hope that this review will give readers a better understanding of the chemistry and basic research for the development of novel antibiotics.
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Affiliation(s)
- Tse-Wei Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
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2
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Abstract
The peptidoglycan sacculus is a net-like polymer that surrounds the cytoplasmic membrane in most bacteria. It is essential to maintain the bacterial cell shape and protect from turgor. The peptidoglycan has a basic composition, common to all bacteria, with species-specific variations that can modify its biophysical properties or the pathogenicity of the bacteria. The synthesis of peptidoglycan starts in the cytoplasm and the precursor lipid II is flipped across the cytoplasmic membrane. The new peptidoglycan strands are synthesised and incorporated into the pre-existing sacculus by the coordinated activities of peptidoglycan synthases and hydrolases. In the model organism Escherichia coli there are two complexes required for the elongation and division. Each of them is regulated by different proteins from both the cytoplasmic and periplasmic sides that ensure the well-coordinated synthesis of new peptidoglycan.
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3
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Galley NF, O'Reilly AM, Roper DI. Prospects for novel inhibitors of peptidoglycan transglycosylases. Bioorg Chem 2014; 55:16-26. [PMID: 24924926 PMCID: PMC4126109 DOI: 10.1016/j.bioorg.2014.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/12/2014] [Accepted: 05/12/2014] [Indexed: 01/07/2023]
Abstract
We examine key aspects of transglycosylase inhibitor design. Low to high throughput assays suitable for transglycosylase drug discovery. Existing chemical start points for transglycosylase active site targeting.
The lack of novel antimicrobial drugs under development coupled with the increasing occurrence of resistance to existing antibiotics by community and hospital acquired infections is of grave concern. The targeting of biosynthesis of the peptidoglycan component of the bacterial cell wall has proven to be clinically valuable but relatively little therapeutic development has been directed towards the transglycosylase step of this process. Advances towards the isolation of new antimicrobials that target transglycosylase activity will rely on the development of the enzymological tools required to identify and characterise novel inhibitors of these enzymes. Therefore, in this article, we review the assay methods developed for transglycosylases and review recent novel chemical inhibitors discovered in relation to both the lipidic substrates and natural product inhibitors of the transglycosylase step.
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Affiliation(s)
- Nicola F Galley
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Amy M O'Reilly
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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4
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Lupoli TJ, Lebar MD, Markovski M, Bernhardt T, Kahne D, Walker S. Lipoprotein activators stimulate Escherichia coli penicillin-binding proteins by different mechanisms. J Am Chem Soc 2013; 136:52-5. [PMID: 24341982 DOI: 10.1021/ja410813j] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In Escherichia coli , the bifunctional penicillin-binding proteins (PBPs), PBP1A and PBP1B, play critical roles in the final stage of peptidoglycan (PG) biosynthesis. These synthetic enzymes each possess a PG glycosyltransferase (PGT) domain and a transpeptidase (TP) domain. Recent genetic experiments have shown that PBP1A and PBP1B each require an outer membrane lipoprotein, LpoA and LpoB, respectively, to function properly in vivo. Here, we use complementary assays to show that LpoA and LpoB each increase the PGT and TP activities of their cognate PBPs, albeit by different mechanisms. LpoA directly increases the rate of the PBP1A TP reaction, which also results in enhanced PGT activity; in contrast, LpoB directly affects PGT domain activity, resulting in enhanced TP activity. These studies demonstrate bidirectional coupling of PGT and TP domain function. Additionally, the transpeptidation assay described here can be applied to study other activators or inhibitors of the TP domain of PBPs, which are validated drug targets.
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Affiliation(s)
- Tania J Lupoli
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
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5
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Lebar MD, Lupoli TJ, Tsukamoto H, May JM, Walker S, Kahne D. Forming cross-linked peptidoglycan from synthetic gram-negative Lipid II. J Am Chem Soc 2013; 135:4632-5. [PMID: 23480167 DOI: 10.1021/ja312510m] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The bacterial cell wall precursor, Lipid II, has a highly conserved structure among different organisms except for differences in the amino acid sequence of the peptide side chain. Here, we report an efficient and flexible synthesis of the canonical Lipid II precursor required for the assembly of Gram-negative peptidoglycan (PG). We use a rapid LC/MS assay to analyze PG glycosyltransfer (PGT) and transpeptidase (TP) activities of Escherichia coli penicillin binding proteins PBP1A and PBP1B and show that the native m-DAP residue in the peptide side chain of Lipid II is required in order for TP-catalyzed peptide cross-linking to occur in vitro. Comparison of PG produced from synthetic canonical E. coli Lipid II with PG isolated from E. coli cells demonstrates that we can produce PG in vitro that resembles native structure. This work provides the tools necessary for reconstituting cell wall synthesis, an essential cellular process and major antibiotic target, in a purified system.
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Affiliation(s)
- Matthew D Lebar
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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6
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Gampe CM, Tsukamoto H, Doud EH, Walker S, Kahne D. Tuning the moenomycin pharmacophore to enable discovery of bacterial cell wall synthesis inhibitors. J Am Chem Soc 2013; 135:3776-9. [PMID: 23448584 DOI: 10.1021/ja4000933] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antibiotic drugs need to be identified to address rapidly developing resistance of bacterial pathogens to common antibiotics. The natural antibiotic moenomycin A is the prototype for compounds that bind to bacterial peptidoglycan glycosyltransferases (PGTs) and inhibit cell wall biosynthesis, but it cannot be used as a drug. Here we report the chemoenzymatic synthesis of a fluorescently labeled, truncated analogue of moenomycin based on the minimal pharmacophore. This probe, which has optimized enzyme binding properties compared to moenomycin, was designed to identify low-micromolar inhibitors that bind to conserved features in PGT active sites. We demonstrate its use in displacement assays using PGTs from S. aureus, E. faecalis, and E. coli. 110,000 compounds were screened against S. aureus SgtB, and we identified a non-carbohydrate based compound that binds to all PGTs tested. We also show that the compound inhibits in vitro formation of peptidoglycan chains by several different PGTs. Thus, this assay enables the identification of small molecules that target PGT active sites, and may provide lead compounds for development of new antibiotics.
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Affiliation(s)
- Christian M Gampe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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7
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Helassa N, Vollmer W, Breukink E, Vernet T, Zapun A. The membrane anchor of penicillin-binding protein PBP2a from Streptococcus pneumoniae influences peptidoglycan chain length. FEBS J 2012; 279:2071-81. [DOI: 10.1111/j.1742-4658.2012.08592.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Lupoli TJ, Tsukamoto H, Doud EH, Wang TSA, Walker S, Kahne D. Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan. J Am Chem Soc 2011; 133:10748-51. [PMID: 21682301 DOI: 10.1021/ja2040656] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The β-lactams are the most important class of antibiotics in clinical use. Their lethal targets are the transpeptidase domains of penicillin binding proteins (PBPs), which catalyze the cross-linking of bacterial peptidoglycan (PG) during cell wall synthesis. The transpeptidation reaction occurs in two steps, the first being formation of a covalent enzyme intermediate and the second involving attack of an amine on this intermediate. Here we use defined PG substrates to dissect the individual steps catalyzed by a purified E. coli transpeptidase. We demonstrate that this transpeptidase accepts a set of structurally diverse D-amino acid substrates and incorporates them into PG fragments. These results provide new information on donor and acceptor requirements as well as a mechanistic basis for previous observations that noncanonical D-amino acids can be introduced into the bacterial cell wall.
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Affiliation(s)
- Tania J Lupoli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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9
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Wang TSA, Lupoli TJ, Sumida Y, Tsukamoto H, Wu Y, Rebets Y, Kahne DE, Walker S. Primer preactivation of peptidoglycan polymerases. J Am Chem Soc 2011; 133:8528-30. [PMID: 21568328 DOI: 10.1021/ja2028712] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidoglycan glycosyltransferases are highly conserved bacterial enzymes that catalyze glycan strand polymerization to build the cell wall. Because the cell wall is essential for bacterial cell survival, these glycosyltransferases are potential antibiotic targets, but a detailed understanding of their mechanisms is lacking. Here we show that a synthetic peptidoglycan fragment that mimics the elongating polymer chain activates peptidoglycan glycosyltransferases by bypassing the rate-limiting initiation step.
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Affiliation(s)
- Tsung-Shing Andrew Wang
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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10
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Macheboeuf P, Piuzzi M, Finet S, Bontems F, Pérez J, Dessen A, Vachette P. Solution X-ray scattering study of a full-length class A penicillin-binding protein. Biochem Biophys Res Commun 2011; 405:107-11. [PMID: 21216228 DOI: 10.1016/j.bbrc.2011.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 01/02/2011] [Indexed: 10/18/2022]
Abstract
Penicillin binding proteins (PBPs) catalyze essential steps in the biosynthesis of peptidoglycan, the main component of the bacterial cell wall. PBPs can harbor two catalytic domains, namely the glycosyltransferase (GT) and transpeptidase (TP) activities, the latter being the target for β-lactam antibiotics. Despite the availability of structural information regarding bi-functional PBPs, little is known regarding the interaction and flexibility between the TP and GT domains. Here, we describe the structural characterization in solution by small angle X-ray scattering (SAXS) of PBP1b, a bi-functional PBP from Streptococcus pneumoniae. The molecule is present in solution as an elongated monomer. Refinement of internal coordinates starting from a homology model yields models in which the two domains are in an extended conformation without any mutual contact compatible with the existence of restricted mobility.
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Affiliation(s)
- P Macheboeuf
- Institut de Biologie Structurale, Bacterial Pathogenesis Group, UMR 5075 (CEA, CNRS, University Joseph Fourier-Grenoble I), Grenoble, France.
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11
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Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
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Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
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12
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Offant J, Terrak M, Derouaux A, Breukink E, Nguyen-Distèche M, Zapun A, Vernet T. Optimization of conditions for the glycosyltransferase activity of penicillin-binding protein 1a from Thermotoga maritima. FEBS J 2010; 277:4290-8. [DOI: 10.1111/j.1742-4658.2010.07817.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Terrak M, Sauvage E, Derouaux A, Dehareng D, Bouhss A, Breukink E, Jeanjean S, Nguyen-Distèche M. Importance of the conserved residues in the peptidoglycan glycosyltransferase module of the class A penicillin-binding protein 1b of Escherichia coli. J Biol Chem 2008; 283:28464-70. [PMID: 18701463 DOI: 10.1074/jbc.m803223200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The peptidoglycan glycosyltransferase (GT) module of class A penicillin-binding proteins (PBPs) and monofunctional GTs catalyze glycan chain elongation of the bacterial cell wall. These enzymes belong to the GT51 family, are characterized by five conserved motifs, and have some fold similarity with the phage lambda lysozyme. In this work, we have systematically modified all the conserved amino acid residues of the GT module of Escherichia coli class A PBP1b by site-directed mutagenesis and determined their importance for the in vivo and in vitro activity and the thermostability of the protein. To get an insight into the GT active site of this paradigm enzyme, a model of PBP1b GT domain was constructed based on the available crystal structures (PDB codes 2OLV and 2OLU). The data show that in addition to the essential glutamate residues Glu233 of motif 1 and Glu290 of motif 3, the residues Phe237 and His240 of motif 1 and Gly264, Thr267, Gln271, and Lys274 of motif 2, all located in the catalytic cavity of the GT domain, are essential for the in vitro enzymatic activity of the PBP1b and for its in vivo functioning. Thus, the first three conserved motifs contain most of the residues that are required for the GT activity of the PBP1b. The residues Asp234, Phe237, His240, Thr267, and Gln271 are proposed to maintain the structure of the active site and the positioning of the catalytic Glu233.
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Affiliation(s)
- Mohammed Terrak
- Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B6a, B-4000 Sart-Tilman, Belgium.
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14
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Abstract
This review is an attempt to bring together and critically evaluate the now-abundant but dispersed data concerning the lipid intermediates of the biosynthesis of bacterial peptidoglycan. Lipid I, lipid II, and their modified forms play a key role not only as the specific link between the intracellular synthesis of the peptidoglycan monomer unit and the extracytoplasmic polymerization reactions but also in the attachment of proteins to the bacterial cell wall and in the mechanisms of action of antibiotics with which they form specific complexes. The survey deals first with their detection, purification, structure, and preparation by chemical and enzymatic methods. The recent important advances in the study of transferases MraY and MurG, responsible for the formation of lipids I and II, are reported. Various modifications undergone by lipids I and II are described, especially those occurring in gram-positive organisms. The following section concerns the cellular location of the lipid intermediates and the translocation of lipid II across the cytoplasmic membrane. The great efforts made since 2000 in the study of the glycosyltransferases catalyzing the glycan chain formation with lipid II or analogues are analyzed in detail. Finally, examples of antibiotics forming complexes with the lipid intermediates are presented.
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15
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Sauvage E, Kerff F, Terrak M, Ayala JA, Charlier P. The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol Rev 2008; 32:234-58. [PMID: 18266856 DOI: 10.1111/j.1574-6976.2008.00105.x] [Citation(s) in RCA: 882] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Eric Sauvage
- Centre d'Ingénierie des Protéines, Institut de Physique B5a et Institut de Chimie B6a, University of Liège, Sart Tilman, Belgium.
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16
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Domain requirement of moenomycin binding to bifunctional transglycosylases and development of high-throughput discovery of antibiotics. Proc Natl Acad Sci U S A 2008; 105:431-6. [PMID: 18182485 DOI: 10.1073/pnas.0710868105] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Moenomycin inhibits bacterial growth by blocking the transglycosylase activity of class A penicillin-binding proteins (PBPs), which are key enzymes in bacterial cell wall synthesis. We compared the binding affinities of moenomycin A with various truncated PBPs by using surface plasmon resonance analysis and found that the transmembrane domain is important for moenomycin binding. Full-length class A PBPs from 16 bacterial species were produced, and their binding activities showed a correlation with the antimicrobial activity of moenomycin against Enterococcus faecalis and Staphylococcus aureus. On the basis of these findings, a fluorescence anisotropy-based high-throughput assay was developed and used successfully for identification of transglycosylase inhibitors.
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17
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Perlstein DL, Zhang Y, Wang TS, Kahne DE, Walker S. The direction of glycan chain elongation by peptidoglycan glycosyltransferases. J Am Chem Soc 2007; 129:12674-5. [PMID: 17914829 PMCID: PMC3206585 DOI: 10.1021/ja075965y] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deborah L Perlstein
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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18
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Vollmer W, Bertsche U. Murein (peptidoglycan) structure, architecture and biosynthesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1778:1714-34. [PMID: 17658458 DOI: 10.1016/j.bbamem.2007.06.007] [Citation(s) in RCA: 307] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 06/11/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
The periplasmic murein (peptidoglycan) sacculus is a giant macromolecule made of glycan strands cross-linked by short peptides completely surrounding the cytoplasmic membrane to protect the cell from lysis due to its internal osmotic pressure. More than 50 different muropeptides are released from the sacculus by treatment with a muramidase. Escherichia coli has six murein synthases which enlarge the sacculus by transglycosylation and transpeptidation of lipid II precursor. A set of twelve periplasmic murein hydrolases (autolysins) release murein fragments during cell growth and division. Recent data on the in vitro murein synthesis activities of the murein synthases and on the interactions between murein synthases, hydrolases and cell cycle related proteins are being summarized. There are different models for the architecture of murein and for the incorporation of new precursor into the sacculus. We present a model in which morphogenesis of the rod-shaped E. coli is driven by cytoskeleton elements competing for the control over the murein synthesis multi-enzyme complexes.
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Affiliation(s)
- Waldemar Vollmer
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
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19
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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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20
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Zhang Y, Fechter EJ, Wang TSA, Barrett D, Walker S, Kahne DE. Synthesis of heptaprenyl-lipid IV to analyze peptidoglycan glycosyltransferases. J Am Chem Soc 2007; 129:3080-1. [PMID: 17323951 PMCID: PMC3222299 DOI: 10.1021/ja069060g] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yi Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Eric J. Fechter
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Tsung-Shing Andrew Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- 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
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
- ;
| | - Daniel E. Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- ;
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21
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Liu H, Wong CH. Characterization of a transglycosylase domain of Streptococcus pneumoniae PBP1b. Bioorg Med Chem 2006; 14:7187-95. [PMID: 16870450 DOI: 10.1016/j.bmc.2006.06.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Revised: 06/16/2006] [Accepted: 06/23/2006] [Indexed: 10/24/2022]
Abstract
Inhibitors of transglycosylases may serve as potent antibiotics that are less prone to resistance development in bacterial pathogens. To facilitate the search of such compounds, a transglycosylase (TGase) domain of the membrane integral multidomain Streptococcus pneumoniae PBP1b was cloned and expressed. This TGase domain was characterized by a substrate-dependent fluorescence coupled enzyme assay and an inhibitor-tethered surface plasmon resonance binding assay. Both assays show that the catalytic efficiency of the domain is comparable to that of the monofunctional transglycosylases, and it is fully active in the absence of other domains. The isolation of the active TGase domain makes it possible to screen for potential antibiotics targeting transglycosylases.
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Affiliation(s)
- Haitian Liu
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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22
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Macheboeuf P, Contreras-Martel C, Job V, Dideberg O, Dessen A. Penicillin binding proteins: key players in bacterial cell cycle and drug resistance processes. FEMS Microbiol Rev 2006; 30:673-91. [PMID: 16911039 DOI: 10.1111/j.1574-6976.2006.00024.x] [Citation(s) in RCA: 320] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial cell division and daughter cell formation are complex mechanisms whose details are orchestrated by at least a dozen different proteins. Penicillin-binding proteins (PBPs), membrane-associated macromolecules which play key roles in the cell wall synthesis process, have been exploited for over 70 years as the targets of the highly successful beta-lactam antibiotics. The increasing incidence of beta-lactam resistant microorganisms, coupled to progress made in genomics, genetics and immunofluorescence microscopy techniques, have encouraged the intensive study of PBPs from a variety of bacterial species. In addition, the recent publication of high-resolution structures of PBPs from pathogenic organisms have shed light on the complex intertwining of drug resistance and cell division processes. In this review, we discuss structural, functional and biological features of such enzymes which, albeit having initially been identified several decades ago, are now being aggressively pursued as highly attractive targets for the development of novel antibiotherapies.
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Affiliation(s)
- Pauline Macheboeuf
- Institut de Biologie Structurale Jean-Pierre Ebel (CNRS/CEA/UJF), UMR 5075, Laboratoire des Protéines Membranaires, Grenoble, France
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23
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Born P, Breukink E, Vollmer W. In vitro synthesis of cross-linked murein and its attachment to sacculi by PBP1A from Escherichia coli. J Biol Chem 2006; 281:26985-93. [PMID: 16840781 DOI: 10.1074/jbc.m604083200] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The penicillin-binding protein (PBP) 1A is a major murein (peptidoglycan) synthase in Escherichia coli. The murein synthesis activity of PBP1A was studied in vitro with radioactive lipid II substrate. PBP1A produced murein glycan strands by transglycosylation and formed peptide cross-links by transpeptidation. Time course experiments revealed that PBP1A, unlike PBP1B, required the presence of polymerized glycan strands carrying monomeric peptides for cross-linking activity. PBP1A was capable of attaching nascent murein synthesized from radioactive lipid II to nonlabeled murein sacculi. The attachment of the new material occurred by transpeptidation reactions in which monomeric triand tetrapeptides in the sacculi were the acceptors.
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Affiliation(s)
- Petra Born
- Mikrobielle Genetik, Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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Yi W, Yao Q, Zhang Y, Motari E, Lin S, Wang PG. The wbnH gene of Escherichia coli O86:H2 encodes an α-1,3-N-acetylgalactosaminyl transferase involved in the O-repeating unit biosynthesis. Biochem Biophys Res Commun 2006; 344:631-9. [PMID: 16630548 DOI: 10.1016/j.bbrc.2006.03.181] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Accepted: 03/24/2006] [Indexed: 11/19/2022]
Abstract
O-repeating unit biosynthesis is the first committed step in lipopolysaccharide (LPS) biosynthesis in a variety of gram-negative bacteria. The wbnH gene was previously proposed to encode a glycosyltransferase involved in O-repeating unit synthesis in Escherichia coli O86:H2 strain. In this work, we provide biochemical evidence to show that wbnH encodes a N-acetylgalactosaminyl transferase (GalNAcT) that catalyzes the transfer of GalNAc from UDP-GalNAc to the GalNAc-pyrophosphate-lipid acceptor. WbnH activity was characterized using a synthetic acceptor substrate GalNAc alpha-PP-O(CH2)11-OPh. The resulting disaccharide product GalNAc-alpha-1,3-GalNAc alpha-PP-O(CH2)11-OPh was analyzed by LC-MS and NMR spectroscopy. Substrate specificity study indicates that pyrophosphate and hydrophobic lipid moiety are structural requirements for WbnH activity. Divalent metal cations are not required for enzyme catalysis, suggesting WbnH belongs to glycosyltransferase GT-B superfamily. Our results complete the characterization of O86 O-unit assembly pathway, and provide the access of chemically defined O-unit substrates for the further investigation of O-antigen biosynthetic mechanism.
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Affiliation(s)
- Wen Yi
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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25
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Offant J, Michoux F, Dermiaux A, Biton J, Bourne Y. Functional characterization of the glycosyltransferase domain of penicillin-binding protein 1a from Thermotoga maritima. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1036-42. [PMID: 16725395 DOI: 10.1016/j.bbapap.2006.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 03/16/2006] [Accepted: 03/23/2006] [Indexed: 11/26/2022]
Abstract
Class A penicillin-binding proteins (A-PBPs) are high-molecular weight membrane-bound bifunctional enzymes that catalyze the penicillin-sensitive transpeptidation and transglycosylation reaction steps involved in peptidoglycan assembling. We have over-expressed and characterized a soluble form of the glycosyltransferase domain of PBP1a (GT-PBP1a*) from the hyperthermophilic bacteria Thermotoga maritima. GT-PBP1a* efficiently catalyses peptidoglycan biosynthesis, as shown using an in vitro biosynthetized dansylated-lipid II substrate and a HPLC-coupled assay, and is specifically inhibited by moenomycin. GT-PBP1a* tends to spontaneously aggregate in detergent-free solution, a feature that supports existence of a secondary site for membrane association, distinct from the N-terminal transmembrane anchoring region. Overall, our preliminary data document the biochemical properties of GT-PBP1a* and should guide further studies aimed at deciphering the structural determinants involved into membrane binding by this class of enzymes.
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Affiliation(s)
- Julien Offant
- Architecture et Fonction des Macromolécules Biologiques, Case 932, Campus de Luminy, F13288 Marseille Cedex 09, France
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26
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Terrak M, Nguyen-Distèche M. Kinetic characterization of the monofunctional glycosyltransferase from Staphylococcus aureus. J Bacteriol 2006; 188:2528-32. [PMID: 16547040 PMCID: PMC1428434 DOI: 10.1128/jb.188.7.2528-2532.2006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Accepted: 01/09/2006] [Indexed: 12/20/2022] Open
Abstract
The glycosyltransferase (GT) module of class A penicillin-binding proteins (PBPs) and monofunctional GTs (MGTs) belong to the GT51 family in the sequence-based classification of GTs. They both possess five conserved motifs and use lipid II precursor (undecaprenyl-pyrophosphate-N-acetylglucosaminyl-N-acetylmuramoyl- pentapeptide) to synthesize the glycan chain of the bacterial wall peptidoglycan. MGTs appear to be dispensable for growth of some bacteria in vitro. However, new evidence shows that they may be essential for the infection process and development of pathogenic bacteria in their hosts. Only a small number of class A PBPs have been characterized so far, and no kinetic data are available on MGTs. In this study, we present the principal enzymatic properties of the Staphylococcus aureus MGT. The enzyme catalyzes glycan chain polymerization with an efficiency of approximately 5,800 M(-1) s(-1) and has a pH optimum of 7.5, and its activity requires metal ions with a maximum observed in the presence of Mn2+. The properties of S. aureus MGT are distinct from those of S. aureus PBP2 and Escherichia coli MGT, but they are similar to those of E. coli PBP1b. We examined the role of the conserved Glu100 of S. aureus MGT (equivalent to the proposed catalytic Glu233 of E. coli PBP1b) by site-directed mutagenesis. The Glu100Gln mutation results in a drastic loss of GT activity. This shows that Glu100 is also critical for catalysis in S. aureus MGT and confirms that the conserved glutamate of the first motif EDXXFXX(H/N)X(G/A) is likely the key catalytic residue in the GT51 active site.
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Affiliation(s)
- Mohammed Terrak
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie, B6a, B-4000 Sart-Tilman, Belgium
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27
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Affiliation(s)
- Peter Welzel
- Institut für Organische Chemie, Universität Leipzig, Germany.
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28
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Ostash B, Walker S. Bacterial transglycosylase inhibitors. Curr Opin Chem Biol 2006; 9:459-66. [PMID: 16118062 DOI: 10.1016/j.cbpa.2005.08.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Accepted: 08/12/2005] [Indexed: 12/01/2022]
Abstract
The spread of bacterial resistance to known antibiotics has inspired interest in previously under-exploited drug targets. The transglycosylation reaction remains a 'black box' in the generally well-studied process of bacterial peptidoglycan biosynthesis, which is a very attractive target for chemotherapeutic intervention. Here, we summarize recent progress in the study of bacterial transglycosylases and the compounds that inhibit them. The transglycosylation reaction is readily targeted by several different classes of natural products, implying that it should be possible to develop drugs that inhibit this process once efficient high-throughput screens and appropriate compound libraries have been developed.
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Affiliation(s)
- Bohdan Ostash
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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29
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Bertsche U, Breukink E, Kast T, Vollmer W. In Vitro Murein (Peptidoglycan) Synthesis by Dimers of the Bifunctional Transglycosylase-Transpeptidase PBP1B from Escherichia coli. J Biol Chem 2005; 280:38096-101. [PMID: 16154998 DOI: 10.1074/jbc.m508646200] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PBP1B is a major bifunctional murein (peptidoglycan) synthase catalyzing transglycosylation and transpeptidation reactions in Escherichia coli. PBP1B has been shown to form dimers in vivo. The K(D) value for PBP1B dimerization was determined by surface plasmon resonance. The effect of the dimerization of PBP1B on its activities was studied with a newly developed in vitro murein synthesis assay with radioactively labeled lipid II precursor as substrate. Under conditions at which PBP1B dimerizes, the enzyme synthesized murein with long glycan strands (>25 disaccharide units) and with almost 50% of the peptides being part of cross-links. PBP1B was also capable of synthesizing trimeric muropeptide structures. Tri-, tetra-, and pentapeptide compounds could serve as acceptors in the PBP1B-catalyzed transpeptidation reaction.
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Affiliation(s)
- Ute Bertsche
- Mikrobielle Genetik, Universität Tübingen, Germany
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Barrett D, Leimkuhler C, Chen L, Walker D, Kahne D, Walker S. Kinetic characterization of the glycosyltransferase module of Staphylococcus aureus PBP2. J Bacteriol 2005; 187:2215-7. [PMID: 15743972 PMCID: PMC1064046 DOI: 10.1128/jb.187.6.2215-2217.2005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the heterologous overexpression and purification of Staphylococcus aureus PBP2 and demonstrate efficient glycan polymerization from lipid II in vitro. S. aureus PBP2 is the first purified gram-positive class A penicillin-binding protein to show good transglycosylase activity. This enables further studies on this important class of enzymes.
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Affiliation(s)
- Dianah Barrett
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
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31
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Walker S, Chen L, Hu Y, Rew Y, Shin D, Boger DL. Chemistry and Biology of Ramoplanin: A Lipoglycodepsipeptide with Potent Antibiotic Activity. Chem Rev 2005; 105:449-76. [PMID: 15700952 DOI: 10.1021/cr030106n] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suzanne Walker
- The Department of Microbiology & Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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