1
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Almufarriji FM, Alotaibi BS, Alamri AS, Alkhalil SS, Alkhorayef N, Hakami MA. Unveiling the multitargeted potential of deprodone and control comparison with linezolid against hydrolase and transferase enzymes of methicillin-resistant Staphylococcus aureus. Int J Biol Macromol 2024; 279:135459. [PMID: 39250989 DOI: 10.1016/j.ijbiomac.2024.135459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 08/27/2024] [Accepted: 09/06/2024] [Indexed: 09/11/2024]
Abstract
Staphylococcus aureus (S. aureus), commonly found on the skin and nose, causes minor skin conditions to life-threatening diseases, including boils or impetigo, pneumonia, and bloodstream infections. MRSA (Methicillin-Resistant S. aureus) is a strain resistant to many antibiotics and poses a significant challenge in clinical settings. Nowadays, the alternative drug Linezolid is used, and it is not clear when MRSA starts resistance to it, necessitating the need for more alternative drugs with the least chance of developing resistance. This study aims to identify a multitargeted drug candidate with better efficacy than Linezolid. We have taken three hydrolase and transferase proteins from S. aureus, performed the multitargeted docking studies with human-approved drugs, and compared them with the control drug Linezolid. The docking and MM\GBSA scores ranging from -6.79 to -5.78 Kcal/mol and - 37.47 to 30.16 Kcal/mol, respectively, that revealed Deprodone (used for inflammatory skin disorders, bowel disease, and fatty acid metabolism disorders) can be a far better and multitargeted drug candidate than Linezolid. We extended our studies to include extensive pharmacokinetics and molecular interaction fingerprints for interaction pattern studies. Also, the DFT computations optimised the drug, and we extended our studies for MD Simulation in water for 100 ns, which showed the complexes among the identified drug with proteins are entirely stable with acceptable deviation, fluctuations and many intermolecular interactions that make them stable. We also performed the MM\GBSA studies on MD simulation's all 1000 frames to understand the complex energy level. All the results reveal promising interactions between Deprodone and the targeted enzymes, suggesting its potential as a multitargeted therapeutic agent-however, experimental studies need to validate Deprodone against MRSA.
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Affiliation(s)
- Fawaz M Almufarriji
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah 19257, Riyadh, Saudi Arabia.
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah 19257, Riyadh, Saudi Arabia.
| | - Ahlam Saleh Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah 19257, Riyadh, Saudi Arabia.
| | - Samia S Alkhalil
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah 19257, Riyadh, Saudi Arabia.
| | - Nada Alkhorayef
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah 19257, Riyadh, Saudi Arabia.
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah 19257, Riyadh, Saudi Arabia.
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2
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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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3
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Rengifo-Lema MJ, Proaño-Bolaños C, Cuesta S, Meneses L. Computational modelling of the antimicrobial peptides Cruzioseptin-4 extracted from the frog Cruziohyla calcarifer and Pictuseptin-1 extracted from the frog Boana picturata. Sci Rep 2024; 14:4805. [PMID: 38413681 PMCID: PMC10899591 DOI: 10.1038/s41598-024-55171-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024] Open
Abstract
A computational study of the peptides Cruzioseptin-4 and Pictuseptin-1, identified in Cruziohyla calcarifer and Boana picturata respectively, has been carried out. The studies on Cruzioseptin-4 show that it is a cationic peptide with a chain of 23 amino acids that possess 52.17% of hydrophobic amino acids and a charge of + 1.2 at pH 7. Similarly, Pictuseptin-1 is a 22 amino acids peptide with a charge of + 3 at pH 7 and 45.45% of hydrophobic amino acids. Furthermore, the predominant secondary structure for both peptides is alpha-helical. The physicochemical properties were predicted using PepCalc and Bio-Synthesis; secondary structures using Jpred4 and PredictProtein; while molecular docking was performed using Autodock Vina. Geometry optimization of the peptides was done using the ONIOM hybrid method with the HF/6-31G basis set implemented in the Gaussian 09 program. Finally, the molecular docking study indicates that the viable mechanism of action for both peptides is through a targeted attack on the cell membrane of pathogens via electrostatic interactions with different membrane components, leading to cell lysis.
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Affiliation(s)
- María José Rengifo-Lema
- Escuela de Ciencias Químicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador
| | | | - Sebastián Cuesta
- Escuela de Ciencias Químicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador
| | - Lorena Meneses
- Escuela de Ciencias Químicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Quito, Ecuador.
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4
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Midonet C, Bisset S, Shlosman I, Cava F, Rudner DZ, Bernhardt TG. MacP bypass variants of Streptococcus pneumoniae PBP2a suggest a conserved mechanism for the activation of bifunctional cell wall synthases. mBio 2023; 14:e0239023. [PMID: 37847021 PMCID: PMC10746261 DOI: 10.1128/mbio.02390-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 10/18/2023] Open
Abstract
IMPORTANCE Class A penicillin-binding proteins (aPBPs) play critical roles in bacterial cell wall biogenesis. As the targets of penicillin, they are among the most important drug targets in history. Although the biochemical activities of these enzymes have been well studied, little is known about how they are regulated in cells to control when and where peptidoglycan is made. In this report, we isolate variants of the Streptococcus pneumoniae enzyme PBP2a that function in cells without MacP, a partner normally required for its activity. The amino acid substitutions activate the cell wall synthase activity of PBP2a, and their location in a model structure suggests an activation mechanism for this enzyme that is shared with aPBPs from distantly related organisms with distinct activators.
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Affiliation(s)
- Caroline Midonet
- Department of Microbiology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts, USA
| | - Sean Bisset
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Irina Shlosman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Umea, Sweden
- Department of Molecular Biology, Science for Life Laboratory (SciLifeLab), Umeå University, Umeå, Sweden
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts, USA
| | - Thomas G. Bernhardt
- Department of Microbiology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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5
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Shlosman I, Fivenson EM, Gilman MSA, Sisley TA, Walker S, Bernhardt TG, Kruse AC, Loparo JJ. Allosteric activation of cell wall synthesis during bacterial growth. Nat Commun 2023; 14:3439. [PMID: 37301887 PMCID: PMC10257715 DOI: 10.1038/s41467-023-39037-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The peptidoglycan (PG) cell wall protects bacteria against osmotic lysis and determines cell shape, making this structure a key antibiotic target. Peptidoglycan is a polymer of glycan chains connected by peptide crosslinks, and its synthesis requires precise spatiotemporal coordination between glycan polymerization and crosslinking. However, the molecular mechanism by which these reactions are initiated and coupled is unclear. Here we use single-molecule FRET and cryo-EM to show that an essential PG synthase (RodA-PBP2) responsible for bacterial elongation undergoes dynamic exchange between closed and open states. Structural opening couples the activation of polymerization and crosslinking and is essential in vivo. Given the high conservation of this family of synthases, the opening motion that we uncovered likely represents a conserved regulatory mechanism that controls the activation of PG synthesis during other cellular processes, including cell division.
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Affiliation(s)
- Irina Shlosman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Elayne M Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Tyler A Sisley
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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6
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Nguyen HTV, Chen X, Parada C, Luo AC, Shih O, Jeng US, Huang CY, Shih YL, Ma C. Structure of the heterotrimeric membrane protein complex FtsB-FtsL-FtsQ of the bacterial divisome. Nat Commun 2023; 14:1903. [PMID: 37019934 PMCID: PMC10076392 DOI: 10.1038/s41467-023-37543-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
The synthesis of the cell-wall peptidoglycan during bacterial cell division is mediated by a multiprotein machine, called the divisome. The essential membrane protein complex of FtsB, FtsL and FtsQ (FtsBLQ) is at the heart of the divisome assembly cascade in Escherichia coli. This complex regulates the transglycosylation and transpeptidation activities of the FtsW-FtsI complex and PBP1b via coordination with FtsN, the trigger for the onset of constriction. Yet the underlying mechanism of FtsBLQ-mediated regulation is largely unknown. Here, we report the full-length structure of the heterotrimeric FtsBLQ complex, which reveals a V-shaped architecture in a tilted orientation. Such a conformation could be strengthened by the transmembrane and the coiled-coil domains of the FtsBL heterodimer, as well as an extended β-sheet of the C-terminal interaction site involving all three proteins. This trimeric structure may also facilitate interactions with other divisome proteins in an allosteric manner. These results lead us to propose a structure-based model that delineates the mechanism of the regulation of peptidoglycan synthases by the FtsBLQ complex.
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Affiliation(s)
- Hong Thuy Vy Nguyen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Xiaorui Chen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Claudia Parada
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - An-Chi Luo
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30044, Taiwan
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Yu-Ling Shih
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.
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7
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Chen YW, Kong WP, Wong KY. The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations. Comput Struct Biotechnol J 2023; 21:2602-2612. [PMID: 37114213 PMCID: PMC10126914 DOI: 10.1016/j.csbj.2023.03.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The FtsQBL is an essential molecular complex sitting midway through bacterial divisome assembly. To visualize and understand its structure, and the consequences of its membrane anchorage, we produced a model of the E. coli complex using the deep-learning prediction utility, AlphaFold 2. The heterotrimeric model was inserted into a 3-lipid model membrane and subjected to a 500-ns atomistic molecular dynamics simulation. The model is superb in quality and captures most experimentally derived structural features, at both the secondary structure and the side-chain levels. The model consists of a uniquely interlocking module contributed by the C-terminal regions of all three proteins. The functionally important constriction control domain residues of FtsB and FtsL are located at a fixed vertical position of ∼43-49 Å from the membrane surface. While the periplasmic domains of all three proteins are well-defined and rigid, the single transmembrane helices of each are flexible and their collective twisting and bending contribute to most structural variations, according to principal component analysis. Considering FtsQ only, the protein is more flexible in its free state relative to its complexed state-with the biggest structural changes located at the elbow between the transmembrane helix and the α-domain. The disordered N-terminal domains of FtsQ and FtsL associate with the cytoplasmic surface of the inner membrane instead of freely venturing into the solvent. Contact network analysis highlighted the formation of the interlocking trimeric module in FtsQBL as playing a central role in mediating the overall structure of the complex.
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8
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Kwan JMC, Qiao Y. Mechanistic Insights into the Activities of Major Families of Enzymes in Bacterial Peptidoglycan Assembly and Breakdown. Chembiochem 2023; 24:e202200693. [PMID: 36715567 DOI: 10.1002/cbic.202200693] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 01/31/2023]
Abstract
Serving as an exoskeletal scaffold, peptidoglycan is a polymeric macromolecule that is essential and conserved across all bacteria, yet is absent in mammalian cells; this has made bacterial peptidoglycan a well-established excellent antibiotic target. In addition, soluble peptidoglycan fragments derived from bacteria are increasingly recognised as key signalling molecules in mediating diverse intra- and inter-species communication in nature, including in gut microbiota-host crosstalk. Each bacterial species encodes multiple redundant enzymes for key enzymatic activities involved in peptidoglycan assembly and breakdown. In this review, we discuss recent findings on the biochemical activities of major peptidoglycan enzymes, including peptidoglycan glycosyltransferases (PGT) and transpeptidases (TPs) in the final stage of peptidoglycan assembly, as well as peptidoglycan glycosidases, lytic transglycosylase (LTs), amidases, endopeptidases (EPs) and carboxypeptidases (CPs) in peptidoglycan turnover and metabolism. Biochemical characterisation of these enzymes provides valuable insights into their substrate specificity, regulation mechanisms and potential modes of inhibition.
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Affiliation(s)
- Jeric Mun Chung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), 21 Nanyang Link, Singapore, 637371, Singapore.,LKC School of Medicine, Nanyang Technological University (NTU) Singapore, 11 Mandalay Road, Singapore, Singapore, 208232, Singapore
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), Singapore, 21 Nanyang Link, Singapore, 637371, Singapore
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9
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Structural diversity, bioactivity, and biosynthesis of phosphoglycolipid family antibiotics: recent advances. BBA ADVANCES 2022; 2:100065. [PMID: 37082588 PMCID: PMC10074958 DOI: 10.1016/j.bbadva.2022.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Moenomycins, such as moenomycin A, are phosphoglycolipid specialized metabolites produced by a number of actinobacterial species. They are among the most potent antibacterial compounds known to date, which drew numerous studies directed at various aspects of the chemistry and biology of moenomycins. In this review, we outline the advances in moenomycin research over the last decade. We focus on biological aspects, highlighting the contribution of the novel methods of genomics and molecular biology to the deciphering of the biosynthesis and activity of moenomycins. Specifically, we describe the structural diversity of moenomycins as well as the underlying genomic variations in moenomycin biosynthetic gene clusters. We also describe the most recent data on the mechanism of action and assembly of complicated phosphoglycolipid scaffold. We conclude with the description of the genetic control of moenomycin production by Streptomyces bacteria and a brief outlook on future developments.
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10
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Kermani AA, Biboy J, Vollmer D, Vollmer W. Outer membrane-anchoring enables LpoB to regulate peptidoglycan synthesis rate. Cell Surf 2022; 8:100086. [PMID: 36304570 PMCID: PMC9593243 DOI: 10.1016/j.tcsw.2022.100086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/25/2022] Open
Abstract
Peptidoglycan (PG) is an essential component of the cell envelope in most bacteria, responsible for maintaining the shape of the cell and protecting the cell from environmental stresses. The growth of the PG layer during cell elongation and division is facilitated by the coordinated activities of PG synthases and hydrolases. PG synthases are regulated from inside the cell by components of the elongasome and divisome complexes driven by the cytoskeletal proteins MreB and FtsZ. In Escherichia coli the PG synthases PBP1A and PBP1B require the activation by outer membrane (OM)-anchored lipoproteins LpoA and LpoB, respectively. These have an elongated structure and are capable to span the periplasm to reach their cognate, cytoplasmic membrane (CM)-anchored PG synthase through the PG layer. Presumably, the Lpo proteins activate the PBPs at sites where the PG mesh is stretched or defective, resulting in coupling of PG synthase activation with cell growth or PG repair. Here we investigated the importance of OM-anchoring on the function of Lpo proteins in regulating PG synthesis in response to environmental stresses. We investigated the effects of an artificially CM-tethered LpoB on cell morphology and PG synthesis. Our results indicate that mis-localization of LpoB affects the growth and morphology of cells in high osmolarity growth medium, and PG synthesis rate upon an osmotic upshift.
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11
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Genetic and Biochemical Characterization of Halogenation and Drug Transportation Genes Encoded in the Albofungin Biosynthetic Gene Cluster. Appl Environ Microbiol 2022; 88:e0080622. [PMID: 36000868 PMCID: PMC9469721 DOI: 10.1128/aem.00806-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Albofungin, a hexacyclic aromatic natural product, exhibits broad-spectrum antimicrobial activity. Its biosynthesis, regulation, and resistance remain elusive. Here, we report the albofungin (abf) biosynthetic gene cluster (BGC) from its producing strain Streptomyces tumemacerans JCM5050. The nascent abf BGC encodes 70 putative genes, including regulators, transporters, type II polyketide synthases (PKSs), oxidoreductase, and tailoring enzymes. To validate the intactness and functionality of the BGC, we developed an Escherichia coli-Streptomyces shuttle bacterial artificial chromosome system, whereby the abf BGC was integrated into the genome of a nonproducing host via heterologous conjugation, wherefrom albofungin can be produced, confirming that the BGC is in effect. We then delimited the boundaries of the BGC by means of in vitro CRISPR-Cas9 DNA editing, concluding a minimal but essential 60-kb abf BGC ranging from orfL to abf58. The orfA gene encoding a reduced flavin adenine dinucleotide (FADH2)-dependent halogenase was examined and is capable of transforming albofungin to halogen-substituted congeners in vivo and in vitro. The orfL gene encoding a transporter was examined in vivo. The presence/absence of orfA or orfL demonstrated that the MIC of albofungin is subject to alteration when an extracellular polysaccharide intercellular adhesin was formed. Despite that halogenation of albofungin somewhat increases binding affinity to transglycosylase (TGase), albofungin with/without a halogen substituent manifests similar in vitro antimicrobial activity. Halogenation, however, limits overall dissemination and effectiveness given a high secretion rate, weak membrane permeability, and high hydrophobicity of the resulting products, whereby the functions of orfA and orfL are correlated with drug detoxification/resistance for the first time. IMPORTANCE Albofungin, a natural product produced from Streptomycetes, exhibits bioactivities against bacteria, fungi, and tumor cells. The biosynthetic logic, regulations, and resistance of albofungin remain yet to be addressed. Herein, the minimal albofungin (abf) biosynthetic gene cluster (BGC) from the producing strain Streptomyces tumemacerans JCM5050 was precisely delimited using the Escherichia coli-Streptomyces shuttle bacterial artificial chromosome system, of which the gene essentiality was established in vivo and in vitro. Next, we characterized two genes orfA and orfL encoded in the abf BGC, which act as a reduced flavin adenine dinucleotide (FADH2)-dependent halogenase and an albofungin-congeners transporter, respectively. While each testing microorganism exhibited different sensitivities to albofungins, the MIC values of albofungins against testing strains with/without orfA and/or orfL were subject to considerable changes. Halogen-substituted albofungins mediated by OrfA manifested overall compromised dissemination and effectiveness, revealing for the first time that two functionally distinct proteins OrfA and OrfL are associated together, exerting a novel “belt and braces” mechanism in antimicrobial detoxification/resistance.
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12
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Photoaffinity labeling of benzophenone-containing salicylanilide compounds to give an insight into the mechanism in disrupting peptidoglycan formation. Bioorg Med Chem 2022; 67:116819. [PMID: 35635930 DOI: 10.1016/j.bmc.2022.116819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022]
Abstract
A series of salicylanilide compounds was previously identified as antibacterial agents that inhibit the peptidoglycan formation. To find the exact binding mode, we synthesized a benzophenone-containing salicylanilide compound (1) and used it as a photoaffinity probe to label Acinetobacter baumannii penicillin-binding protein (PBP1b). After incubation and photo-irradiation, the labeled protein was subjected to trypsin digestion, dialysis enrichment, LC-ESI-MS/MS analysis, and Mascot search to reveal an octadecapeptide sequence 364RQLRTEYQESDLTNQGLR381 that was labeled at E372. Our molecular docking experiments suggest a hydrophobic pocket surrounded by R367 and E372 is the binding site of salicylanilide 1. The pocket lies in between the transglycosylase and transpeptidase domains, thus binding of salicylanilide 1 can block the propagation pathway to disrupt the growth of peptidoglycan chain.
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13
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Della-Felice F, de Andrade Bartolomeu A, Pilli RA. The phosphate ester group in secondary metabolites. Nat Prod Rep 2022; 39:1066-1107. [PMID: 35420073 DOI: 10.1039/d1np00078k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2000 to mid-2021The phosphate ester is a versatile, widespread functional group involved in a plethora of biological activities. Its presence in secondary metabolites, however, is relatively rare compared to other functionalities and thus is part of a rather unexplored chemical space. Herein, the chemistry of secondary metabolites containing the phosphate ester group is discussed. The text emphasizes their structural diversity, biological and pharmacological profiles, and synthetic approaches employed in the phosphorylation step during total synthesis campaigns, covering the literature from 2000 to mid-2021.
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Affiliation(s)
- Franco Della-Felice
- Institute of Chemistry, University of Campinas (UNICAMP), P.O. Box 6154, CEP 13083-970 Campinas, Sao Paulo, Brazil.,Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain.
| | | | - Ronaldo Aloise Pilli
- Institute of Chemistry, University of Campinas (UNICAMP), P.O. Box 6154, CEP 13083-970 Campinas, Sao Paulo, Brazil
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14
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Attaibi M, den Blaauwen T. An Updated Model of the Divisome: Regulation of the Septal Peptidoglycan Synthesis Machinery by the Divisome. Int J Mol Sci 2022; 23:3537. [PMID: 35408901 PMCID: PMC8998562 DOI: 10.3390/ijms23073537] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
The synthesis of a peptidoglycan septum is a fundamental part of bacterial fission and is driven by a multiprotein dynamic complex called the divisome. FtsW and FtsI are essential proteins that synthesize the peptidoglycan septum and are controlled by the regulatory FtsBLQ subcomplex and the activator FtsN. However, their mode of regulation has not yet been uncovered in detail. Understanding this process in detail may enable the development of new compounds to combat the rise in antibiotic resistance. In this review, recent data on the regulation of septal peptidoglycan synthesis is summarized and discussed. Based on structural models and the collected data, multiple putative interactions within FtsWI and with regulators are uncovered. This elaborates on and supports an earlier proposed model that describes active and inactive conformations of the septal peptidoglycan synthesis complex that are stabilized by these interactions. Furthermore, a new model on the spatial organization of the newly synthesized peptidoglycan and the synthesis complex is presented. Overall, the updated model proposes a balance between several allosteric interactions that determine the state of septal peptidoglycan synthesis.
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Affiliation(s)
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
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15
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Wang H, An J, Fan C, Zhai Z, Zhang H, Hao Y. Transcriptome analysis revealed growth phase-associated changes of a centenarian-originated probiotic Bifidobacterium animalis subsp. lactis A6. BMC Microbiol 2022; 22:61. [PMID: 35209838 PMCID: PMC8876546 DOI: 10.1186/s12866-022-02474-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022] Open
Abstract
Background The physiology and application characteristics of probiotics are closely associated with the growth phase. Bifidobacterium animalis subsp. lactis A6 is a promising probiotic strain isolated from the feces of a healthy centenarian in China. In this study, RNA-seq was carried out to investigate the metabolic mechanism between the exponential and the stationary phase in B. lactis A6. Results Differential expression analysis showed that a total of 815 genes were significantly changed in the stationary phase compared to the exponential phase, which consisted of 399 up-regulated and 416 down-regulated genes. The results showed that the transport and metabolism of cellobiose, xylooligosaccharides and raffinose were enhanced at the stationary phase, which expanded carbon source utilizing profile to confront with glucose consumption. Meanwhile, genes involved in cysteine-cystathionine-cycle (CCC) pathway, glutamate dehydrogenase, branched-chain amino acids (BCAAs) biosynthesis, and Clp protease were all up-regulated in the stationary phase, which may enhance the acid tolerance of B. lactis A6 during stationary phase. Acid tolerance assay indicated that the survival rate of stationary phase cells was 51.07% after treatment by pH 3.0 for 2h, which was 730-fold higher than that of 0.07% with log phase cells. In addition, peptidoglycan biosynthesis was significantly repressed, which is comparable with the decreased growth rate during the stationary phase. Remarkably, a putative gene cluster encoding Tad pili was up-regulated by 6.5 to 12.1-fold, which is consistent with the significantly increased adhesion rate to mucin from 2.38% to 4.90% during the transition from the exponential phase to the stationary phase. Conclusions This study reported growth phase-associated changes of B. lactis A6 during fermentation, including expanded carbon source utilizing profile, enhanced acid tolerance, and up-regulated Tad pili gene cluster responsible for bacterial adhesion in the stationary phase. These findings provide a novel insight into the growth phase associated characteristics in B. lactis A6 and provide valuable information for further application in the food industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02474-5.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China
| | - Jieran An
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China
| | - Chengfei Fan
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China
| | - Zhengyuan Zhai
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hongxing Zhang
- Department of Food Science, Beijing University of Agriculture, 7 Bei Nong Road, Changping District, Beijing, 102206, China
| | - Yanling Hao
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
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16
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Hsieh PY, Meng FC, Guo CW, Hu KH, Shih YL, Cheng WC. Harnessing Fluorescent Moenomycin A Antibiotics for Bacterial Cell Wall Imaging Studies. Chembiochem 2021; 22:3462-3468. [PMID: 34606179 DOI: 10.1002/cbic.202100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/30/2021] [Indexed: 11/11/2022]
Abstract
The imaging of peptidoglycan (PGN) dynamics in living bacteria facilitates the understanding of PGN biosynthesis and wall-targeting antibiotics. The main tools for imaging bacterial PGN are fluorescent probes, such as the well-known PGN metabolic labeling probes. However, fluorescent small-molecule probes for labeling key PGN-synthesizing enzymes, especially for transglycosylases (TGases), remain to be explored. In this work, the first imaging probe for labeling TGase in bacterial cell wall studies is reported. We synthesized various fluorescent MoeA-based molecules by derivatizing the natural antibiotic moenomycin A (MoeA), and used them to label TGases in living bacteria, monitor bacterial growth and division cycles by time-lapse imaging, and study cell wall growth in the mecA-carrying methicillin-resistant Staphylococcus aureus (MRSA) strains when the β-lactam-based probes were unsuitable.
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Affiliation(s)
- Pei-Yu Hsieh
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan
| | - Fan-Chun Meng
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan
| | - Chih-Wei Guo
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan
| | - Kung-Hsiang Hu
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan
| | - Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106, Taiwan.,Department of Microbiology, College of Medicine, National Taiwan University, No.1, Sec 1. Jen Ai Rd., Taipei, 100, Taiwan
| | - Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan.,Department of Chemistry, National Cheng Kung University, No.1, University Road, Tainan, 701, Taiwan.,Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Road, Chiayi, 600, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No.100, Shin-Chuan 1st Road, Kaohsiung, 807, Taiwan
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17
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Hsu TW, Fang JM. Effective assay of bacterial transglycosylation by molecular turn-on sensing and a second-order scattering effect. Analyst 2021; 146:5843-5847. [PMID: 34570849 DOI: 10.1039/d1an00941a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Instead of using the lipid II substrate that requires prior labelling with a radioactive isotope or fluorophore to probe the formation of peptidoglycan in bacterial transglycosylation, the released undecaprenyl pyrophosphate (UPP) product is quantitatively measured either using a terpyridine-zinc fluorescence turn-on sensor or simply by the second-order scattering effect of the in situ formed UPP-calcium complex. Both the assay methods are utilized to identify moenomycin A as a potent transglycosylase inhibitor with a consistent IC50 value.
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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. .,The Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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18
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The LpoA activator is required to stimulate the peptidoglycan polymerase activity of its cognate cell wall synthase PBP1a. Proc Natl Acad Sci U S A 2021; 118:2108894118. [PMID: 34429361 PMCID: PMC8536351 DOI: 10.1073/pnas.2108894118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A cell wall made of the heteropolymer peptidoglycan (PG) surrounds most bacterial cells. This essential surface layer is required to prevent lysis from internal osmotic pressure. The class A penicillin-binding proteins (aPBPs) play key roles in building the PG network. These bifunctional enzymes possess both PG glycosyltransferase (PGT) and transpeptidase (TP) activity to polymerize the wall glycans and cross-link them, respectively. In Escherichia coli and other gram-negative bacteria, aPBP function is dependent on outer membrane lipoproteins. The lipoprotein LpoA activates PBP1a and LpoB promotes PBP1b activity. In a purified system, the major effect of LpoA on PBP1a is TP stimulation. However, the relevance of this activation to the cellular function of LpoA has remained unclear. To better understand why PBP1a requires LpoA for its activity in cells, we identified variants of PBP1a from E. coli and Pseudomonas aeruginosa that function in the absence of the lipoprotein. The changes resulting in LpoA bypass map to the PGT domain and the linker region between the two catalytic domains. Purification of the E. coli variants showed that they are hyperactivated for PGT but not TP activity. Furthermore, in vivo analysis found that LpoA is necessary for the glycan synthesis activity of PBP1a in cells. Thus, our results reveal that LpoA exerts a much greater control over the cellular activity of PBP1a than previously appreciated. It not only modulates PG cross-linking but is also required for its cognate synthase to make PG glycans in the first place.
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Abstract
Most bacteria are surrounded by a peptidoglycan cell wall that defines their shape and protects them from osmotic lysis. The expansion and division of this structure therefore plays an integral role in bacterial growth and division. Additionally, the biogenesis of the peptidoglycan layer is the target of many of our most effective antibiotics. Thus, a better understanding of how the cell wall is built will enable the development of new therapies to combat the rise of drug-resistant bacterial infections. This review covers recent advances in defining the mechanisms involved in assembling the peptidoglycan layer with an emphasis on discoveries related to the function and regulation of the cell elongation and division machineries in the model organisms Escherichia coli and Bacillus subtilis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Patricia D A Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Current affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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20
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Aliashkevich A, Cava F. LD-transpeptidases: the great unknown among the peptidoglycan cross-linkers. FEBS J 2021; 289:4718-4730. [PMID: 34109739 DOI: 10.1111/febs.16066] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/05/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022]
Abstract
The peptidoglycan (PG) cell wall is an essential polymer for the shape and viability of bacteria. Its protective role is in great part provided by its mesh-like character. Therefore, PG-cross-linking enzymes like the penicillin-binding proteins (PBPs) are among the best targets for antibiotics. However, while PBPs have been in the spotlight for more than 50 years, another class of PG-cross-linking enzymes called LD-transpeptidases (LDTs) seemed to contribute less to PG synthesis and, thus, has kept an aura of mystery. In the last years, a number of studies have associated LDTs with cell wall adaptation to stress including β-lactam antibiotics, outer membrane stability, and toxin delivery, which has shed light onto the biological meaning of these proteins. Furthermore, as some species display a great abundance of LD-cross-links in their cell wall, it has been hypothesized that LDTs could also be the main synthetic PG-transpeptidases in some bacteria. In this review, we introduce these enzymes and their role in PG biosynthesis and we highlight the most recent advances in understanding their biological role in diverse species.
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Affiliation(s)
- Alena Aliashkevich
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Sweden
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21
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Huang Y, Chen W, Chung J, Yin J, Yoon J. Recent progress in fluorescent probes for bacteria. Chem Soc Rev 2021; 50:7725-7744. [PMID: 34013918 DOI: 10.1039/d0cs01340d] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Food fermentation, antibiotics, and pollutant degradation are closely related to bacteria. Bacteria play an irreplaceable role in life. However, some bacteria seriously threaten human health and cause large-scale infectious diseases. Therefore, there is a pressing need to develop strategies to accurately monitor bacteria. Technology based on molecular probes and fluorescence imaging is noninvasive, results in little damage, and has high specificity and sensitivity, so it has been widely applied in the detection of bacteria. In this review, we summarize the recent progress in bacterial detection using fluorescence. In particular, we generalize the mechanisms commonly used to design organic fluorescent probes for detecting and imaging bacteria. Moreover, a perspective regarding fluorescent probes for bacterial detection is discussed.
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Affiliation(s)
- Yurou Huang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Weijie Chen
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Jeewon Chung
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyon-Dong, Sodaemun-Ku, Seoul 120-750, Korea.
| | - Jun Yin
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Juyoung Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyon-Dong, Sodaemun-Ku, Seoul 120-750, Korea.
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22
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Wang Y, Liang Z, Zheng Y, Leung ASL, Yan SC, So PK, Leung YC, Wong WL, Wong KY. Rational structural modification of the isatin scaffold to develop new and potent antimicrobial agents targeting bacterial peptidoglycan glycosyltransferase. RSC Adv 2021; 11:18122-18130. [PMID: 35480164 PMCID: PMC9033243 DOI: 10.1039/d1ra02119b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
A series of isatin derivatives bearing three different substituent groups at the N-1, C-3 and C-5 positions of the isatin scaffold were systematically designed and synthesized to study the structure-activity relationship of their inhibition of bacterial peptidoglycan glycosyltransferase (PGT) activity and antimicrobial susceptibility against S. aureus, E. coli and methicillin-resistant Staphylococcus aureus (MRSA (BAA41)) strains. The substituents at these sites are pointing towards three different directions from the isatin scaffold to interact with the amino acid residues in the binding pocket of PGT. Comparative studies of their structure-activity relationship allow us to gain better understanding of the direction of the substituents that contribute critical interactions leading to inhibition activity against the bacterial enzyme. Our results indicate that the modification of these sites is able to maximize the antimicrobial potency and inhibitory action against the bacterial enzyme. Two compounds show good antimicrobial potency (MIC = 3 μg mL-1 against S. aureus and MRSA; 12-24 μg mL-1 against E. coli). Results of the inhibition study against the bacterial enzyme (E. coli PBP 1b) reveal that some compounds are able to achieve excellent in vitro inhibitions of bacterial enzymatic activity (up to 100%). The best half maximal inhibitory concentration (IC50) observed among the new compounds is 8.9 μM.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Zhiguang Liang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Yuanyuan Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Alan Siu-Lun Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Siu-Cheong Yan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Pui-Kin So
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Yun-Chung Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
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23
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CryoEM structure of the antibacterial target PBP1b at 3.3 Å resolution. Nat Commun 2021; 12:2775. [PMID: 33986273 PMCID: PMC8119973 DOI: 10.1038/s41467-021-23063-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/25/2021] [Indexed: 12/02/2022] Open
Abstract
The pathway for the biosynthesis of the bacterial cell wall is one of the most prolific antibiotic targets, exemplified by the widespread use of β-lactam antibiotics. Despite this, our structural understanding of class A penicillin binding proteins, which perform the last two steps in this pathway, is incomplete due to the inherent difficulty in their crystallization and the complexity of their substrates. Here, we determine the near atomic resolution structure of the 83 kDa class A PBP from Escherichia coli, PBP1b, using cryogenic electron microscopy and a styrene maleic acid anhydride membrane mimetic. PBP1b, in its apo form, is seen to exhibit a distinct conformation in comparison to Moenomycin-bound crystal structures. The work herein paves the way for the use of cryoEM in structure-guided antibiotic development for this notoriously difficult to crystalize class of proteins and their complex substrates. Our structural understanding of class A penicillin binding proteins is incomplete due to the difficulty in their crystallization and the complexity of their substrates. Here, authors determine the structure of the 83 kDa class A PBP from Escherichia coli, PBP1b, using cryogenic electron microscopy and a styrene maleic acid anhydride membrane mimetic.
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24
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Erickson HP. How Teichoic Acids Could Support a Periplasm in Gram-Positive Bacteria, and Let Cell Division Cheat Turgor Pressure. Front Microbiol 2021; 12:664704. [PMID: 34040598 PMCID: PMC8141598 DOI: 10.3389/fmicb.2021.664704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022] Open
Abstract
The cytoplasm of bacteria is maintained at a higher osmolality than the growth medium, which generates a turgor pressure. The cell membrane (CM) cannot support a large turgor, so there are two possibilities for transferring the pressure to the peptidoglycan cell wall (PGW): (1) the CM could be pressed directly against the PGW, or (2) the CM could be separated from the PGW by a periplasmic space that is isoosmotic with the cytoplasm. There is strong evidence for gram-negative bacteria that a periplasm exists and is isoosmotic with the cytoplasm. No comparable studies have been done for gram-positive bacteria. Here I suggest that a periplasmic space is probably essential in order for the periplasmic proteins to function, including especially the PBPs that remodel the peptidoglycan wall. I then present a semi-quantitative analysis of how teichoic acids could support a periplasm that is isoosmotic with the cytoplasm. The fixed anionic charge density of teichoic acids in the periplasm is ∼0.5 M, which would bring in ∼0.5 M Na+ neutralizing ions. This approximately balances the excess osmolality of the cytoplasm that would produce a turgor pressure of 19 atm. The 0.5 M fixed charge density is similar to that of proteoglycans in articular cartilage, suggesting a comparability ability to support pressure. An isoosmotic periplasm would be especially important for cell division, since it would allow CM constriction and PGW synthesis to avoid turgor pressure.
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Affiliation(s)
- Harold P Erickson
- Department of Cell Biology, Duke University Medical Center, Durham, NC, United States
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25
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Pazos M, Vollmer W. Regulation and function of class A Penicillin-binding proteins. Curr Opin Microbiol 2021; 60:80-87. [PMID: 33611146 DOI: 10.1016/j.mib.2021.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/09/2021] [Accepted: 01/22/2021] [Indexed: 01/14/2023]
Abstract
Most bacteria surround their cell membrane with a peptidoglycan sacculus that counteracts the turgor and maintains the shape of the cell. Class A PBPs are bi-functional glycosyltransferase-transpeptidases that polymerize glycan chains and cross-link peptides. They have a major contribution to the total peptidoglycan synthesized during cell growth and cell division. In recent years it became apparent that class A PBPs participate in multiple protein? protein interactions and that some of these regulate their activities. In this opinion article, we review and discuss the role of class A PBPs in peptidoglycan growth and repair. We hypothesize that class A PBP function is essential in walled bacteria unless they have (a) SEDS protein(s) capable of replacing their function.
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Affiliation(s)
- Manuel Pazos
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom.
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26
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Garde S, Chodisetti PK, Reddy M. Peptidoglycan: Structure, Synthesis, and Regulation. EcoSal Plus 2021; 9:eESP-0010-2020. [PMID: 33470191 PMCID: PMC11168573 DOI: 10.1128/ecosalplus.esp-0010-2020] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Indexed: 02/06/2023]
Abstract
Peptidoglycan is a defining feature of the bacterial cell wall. Initially identified as a target of the revolutionary beta-lactam antibiotics, peptidoglycan has become a subject of much interest for its biology, its potential for the discovery of novel antibiotic targets, and its role in infection. Peptidoglycan is a large polymer that forms a mesh-like scaffold around the bacterial cytoplasmic membrane. Peptidoglycan synthesis is vital at several stages of the bacterial cell cycle: for expansion of the scaffold during cell elongation and for formation of a septum during cell division. It is a complex multifactorial process that includes formation of monomeric precursors in the cytoplasm, their transport to the periplasm, and polymerization to form a functional peptidoglycan sacculus. These processes require spatio-temporal regulation for successful assembly of a robust sacculus to protect the cell from turgor and determine cell shape. A century of research has uncovered the fundamentals of peptidoglycan biology, and recent studies employing advanced technologies have shed new light on the molecular interactions that govern peptidoglycan synthesis. Here, we describe the peptidoglycan structure, synthesis, and regulation in rod-shaped bacteria, particularly Escherichia coli, with a few examples from Salmonella and other diverse organisms. We focus on the pathway of peptidoglycan sacculus elongation, with special emphasis on discoveries of the past decade that have shaped our understanding of peptidoglycan biology.
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Affiliation(s)
- Shambhavi Garde
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Pavan Kumar Chodisetti
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
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27
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Boes A, Kerff F, Herman R, Touze T, Breukink E, Terrak M. The bacterial cell division protein fragment EFtsN binds to and activates the major peptidoglycan synthase PBP1b. J Biol Chem 2020; 295:18256-18265. [PMID: 33109614 PMCID: PMC7939390 DOI: 10.1074/jbc.ra120.015951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
Peptidoglycan (PG) is an essential constituent of the bacterial cell wall. During cell division, the machinery responsible for PG synthesis localizes mid-cell, at the septum, under the control of a multiprotein complex called the divisome. In Escherichia coli, septal PG synthesis and cell constriction rely on the accumulation of FtsN at the division site. Interestingly, a short sequence of FtsN (Leu75-Gln93, known as EFtsN) was shown to be essential and sufficient for its functioning in vivo, but what exactly this sequence is doing remained unknown. Here, we show that EFtsN binds specifically to the major PG synthase PBP1b and is sufficient to stimulate its biosynthetic glycosyltransferase (GTase) activity. We also report the crystal structure of PBP1b in complex with EFtsN, which demonstrates that EFtsN binds at the junction between the GTase and UB2H domains of PBP1b. Interestingly, mutations to two residues (R141A/R397A) within the EFtsN-binding pocket reduced the activation of PBP1b by FtsN but not by the lipoprotein LpoB. This mutant was unable to rescue the ΔponB-ponAts strain, which lacks PBP1b and has a thermosensitive PBP1a, at nonpermissive temperature and induced a mild cell-chaining phenotype and cell lysis. Altogether, the results show that EFtsN interacts with PBP1b and that this interaction plays a role in the activation of its GTase activity by FtsN, which may contribute to the overall septal PG synthesis and regulation during cell division.
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Affiliation(s)
- Adrien Boes
- InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium
| | - Frederic Kerff
- InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium
| | - Raphael Herman
- InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium
| | - Thierry Touze
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mohammed Terrak
- InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium.
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28
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Kleynhans J, Kruger HG, Cloete T, Zeevaart JR, Ebenhan T. In Silico Modelling in the Development of Novel Radiolabelled Peptide Probes. Curr Med Chem 2020; 27:7048-7063. [DOI: 10.2174/0929867327666200504082256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
Abstract
This review describes the usefulness of in silico design approaches in the design of
new radiopharmaceuticals, especially peptide-based radiotracers (including peptidomimetics).
Although not part of the standard arsenal utilized during radiopharmaceutical design, the use
of in silico strategies is steadily increasing in the field of radiochemistry as it contributes to a
more rational and scientific approach. The development of new peptide-based radiopharmaceuticals
as well as a short introduction to suitable computational approaches are provided in
this review. The first section comprises a concise overview of the three most useful computeraided
drug design strategies used, namely i) a Ligand-based Approach (LBDD) using pharmacophore
modelling, ii) a Structure-based Design Approach (SBDD) using molecular docking
strategies and iii) Absorption-Distribution-Metabolism-Excretion-Toxicity (ADMET)
predictions. The second section summarizes the challenges connected to these computer-aided
techniques and discusses successful applications of in silico radiopharmaceutical design in
peptide-based radiopharmaceutical development, thereby improving the clinical procedure in
Nuclear Medicine. Finally, the advances and future potential of in silico modelling as a design
strategy is highlighted.
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Affiliation(s)
- Janke Kleynhans
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
| | | | - Theunis Cloete
- Center of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
| | - Jan Rijn Zeevaart
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
| | - Thomas Ebenhan
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
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29
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Goossens K, Neves RP, Fernandes PA, De Winter H. A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. J Chem Inf Model 2020; 60:5513-5528. [PMID: 32786224 DOI: 10.1021/acs.jcim.0c00377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacterial glycosyltransferases of the GT51 family are key enzymes in bacterial cell wall synthesis. Inhibiting cell wall synthesis is a very effective approach for development of antibiotics, as this can lead to either bacteriostatic or bactericidal effects. Even though the existence of this family has been known for over 50 years, only one potent inhibitor exists, which is an analog of the lipid IV product and derived from a natural product. Drug development focused on bacterial transglycosylase has been hampered due to little being know about its structure and reaction mechanism. In this study, Staphylococcus aureus monoglycosyltransferase was investigated at an atomistic level using computational methods. Classical molecular dynamics simulations were used to reveal information about the large-scale dynamics of the enzyme-substrate complex and the importance of magnesium in structure and function of the protein, while mixed mode quantum mechanics/molecular mechanics calculations unveiled a novel hypothesis for the reaction mechanism. From these results, we present a new model for the binding mode of lipid II and the reaction mechanism of the GT51 glycosyltransferases. A metal-bound hydroxide catalyzed reaction mechanism yields an estimated free energy barrier of 16.1 ± 1.0 kcal/mol, which is in line with experimental values. The importance of divalent cations is also further discussed. These findings could significantly aid targeted drug design, particularly the efficient development of transition state analogues as potential inhibitors for the GT51 glycosyltransferases.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Rui Pp Neves
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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30
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Abstract
Bacteria surround their cell membrane with a net-like peptidoglycan layer, called sacculus, to protect the cell from bursting and maintain its cell shape. Sacculus growth during elongation and cell division is mediated by dynamic and transient multiprotein complexes, the elongasome and divisome, respectively. In this Review we present our current understanding of how peptidoglycan synthases are regulated by multiple and specific interactions with cell morphogenesis proteins that are linked to a dynamic cytoskeletal protein, either the actin-like MreB or the tubulin-like FtsZ. Several peptidoglycan synthases and hydrolases require activation by outer-membrane-anchored lipoproteins. We also discuss how bacteria achieve robust cell wall growth under different conditions and stresses by maintaining multiple peptidoglycan enzymes and regulators as well as different peptidoglycan growth mechanisms, and we present the emerging role of LD-transpeptidases in peptidoglycan remodelling.
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31
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Boes A, Brunel JM, Derouaux A, Kerff F, Bouhss A, Touze T, Breukink E, Terrak M. Squalamine and Aminosterol Mimics Inhibit the Peptidoglycan Glycosyltransferase Activity of PBP1b. Antibiotics (Basel) 2020; 9:antibiotics9070373. [PMID: 32630634 PMCID: PMC7400108 DOI: 10.3390/antibiotics9070373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Peptidoglycan (PG) is an essential polymer of the bacterial cell wall and a major antibacterial target. Its synthesis requires glycosyltransferase (GTase) and transpeptidase enzymes that, respectively, catalyze glycan chain elongation and their cross-linking to form the protective sacculus of the bacterial cell. The GTase domain of bifunctional penicillin-binding proteins (PBPs) of class A, such as Escherichia coli PBP1b, belong to the GTase 51 family. These enzymes play an essential role in PG synthesis, and their specific inhibition by moenomycin was shown to lead to bacterial cell death. In this work, we report that the aminosterol squalamine and mimic compounds present an unexpected mode of action consisting in the inhibition of the GTase activity of the model enzyme PBP1b. In addition, selected compounds were able to specifically displace the lipid II from the active site in a fluorescence anisotropy assay, suggesting that they act as competitive inhibitors.
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Affiliation(s)
- Adrien Boes
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Jean Michel Brunel
- UMR_MD1, U-1261, Aix Marseille Univ, INSERM, SSA, MCT, 13385 Marseille, France;
| | - Adeline Derouaux
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Frédéric Kerff
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (A.B.); (T.T.)
- Laboratoire Structure-Activite des Biomolecules Normales et Pathologiques (SABNP), Univ Evry, INSERM U1204, Universite Paris-Saclay, 91025 Evry, France
| | - Thierry Touze
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (A.B.); (T.T.)
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Mohammed Terrak
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
- Correspondence: ; Tel.: +33-4366-3332
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32
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Wang Y, Cheong WL, Liang Z, So LY, Chan KF, So PK, Chen YW, Wong WL, Wong KY. Hydrophobic substituents on isatin derivatives enhance their inhibition against bacterial peptidoglycan glycosyltransferase activity. Bioorg Chem 2020; 97:103710. [DOI: 10.1016/j.bioorg.2020.103710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
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33
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Cochrane SA, Lohans CT. Breaking down the cell wall: Strategies for antibiotic discovery targeting bacterial transpeptidases. Eur J Med Chem 2020; 194:112262. [PMID: 32248005 DOI: 10.1016/j.ejmech.2020.112262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022]
Abstract
The enzymes involved in bacterial cell wall synthesis are established antibiotic targets, and continue to be a central focus for antibiotic development. Bacterial penicillin-binding proteins (and, in some bacteria, l,d-transpeptidases) form essential peptide cross-links in the cell wall. Although the β-lactam class of antibiotics target these enzymes, bacterial resistance threatens their clinical use, and there is an urgent unmet need for new antibiotics. However, the search for new antibiotics targeting the bacterial cell wall is hindered by a number of obstacles associated with screening the enzymes involved in peptidoglycan synthesis. This review describes recent approaches for measuring the activity and inhibition of penicillin-binding proteins and l,d-transpeptidases, highlighting strategies that are poised to serve as valuable tools for high-throughput screening of transpeptidase inhibitors, supporting the development of new antibiotics.
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Affiliation(s)
- Stephen A Cochrane
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen's University Belfast, Belfast, BT9 5AG, UK.
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada.
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34
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Issakhanian L, Behzadi P. Antimicrobial Agents and Urinary Tract Infections. Curr Pharm Des 2020; 25:1409-1423. [PMID: 31218955 DOI: 10.2174/1381612825999190619130216] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023]
Abstract
Urinary Tract Infections (UTIs); second-ranking infectious diseases are regarded as a significant global health care problem. The UTIs annually cost tens of millions of dollars for governments worldwide. The main reason behind these costs is incorrect or indefinite treatment. There are a wide range of gram-negative and grampositive bacteria which may cause UTIs in males and females, children and adults. Among gram-negative bacteria, some members of Enterobacteriaceae such as Escherichia coli (E.coli) strains have significant contribution in UTIs. Uropathogenic E.coli (UPEC) strains are recognized as typical bacterial agents for UTIs. Thus, sharp and accurate diagnostic tools are needed for detection and identification of the microbial causative agents of UTIs. In parallel with the utilization of suitable diagnostic methods-to reduce the number of UTIs, effective and definite treatment procedures are needed. Therefore, the prescription of accurate, specific and effective antibiotics and drugs may lead to a definite treatment. However, there are many cases related to UTIs which can be relapsed. Due to a diversity of opportunistic and pathogenic causative microbial agents of UTIs, the treatment procedures should be achieved by the related antimicrobial agents. In this review, common and effective antimicrobial agents which are often prescribed for UTIs caused by UPEC will be discussed. Moreover, we will have a sharp look at their (antimicrobials) molecular treatment mechanisms.
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Affiliation(s)
| | - Payam Behzadi
- Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
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35
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Catherwood AC, Lloyd AJ, Tod JA, Chauhan S, Slade SE, Walkowiak GP, Galley NF, Punekar AS, Smart K, Rea D, Evans ND, Chappell MJ, Roper DI, Dowson CG. Substrate and Stereochemical Control of Peptidoglycan Cross-Linking by Transpeptidation by Escherichia coli PBP1B. J Am Chem Soc 2020; 142:5034-5048. [DOI: 10.1021/jacs.9b08822] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Cross KL, Campbell JH, Balachandran M, Campbell AG, Cooper SJ, Griffen A, Heaton M, Joshi S, Klingeman D, Leys E, Yang Z, Parks JM, Podar M. Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. Nat Biotechnol 2019; 37:1314-1321. [PMID: 31570900 PMCID: PMC6858544 DOI: 10.1038/s41587-019-0260-6] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 08/15/2019] [Indexed: 12/16/2022]
Abstract
Most microorganisms from all taxonomic levels are uncultured. Single-cell
genomes and metagenomes continue to increase the known diversity of
Bacteria and Archaea, but while
‘omics can be used to infer physiological or ecological roles for species
in a community, most of those hypothetical roles remain unvalidated. Here we
report an approach to capture specific microorganisms from complex communities
into pure cultures using genome-informed antibody engineering. We apply our
reverse genomics approach to isolate and sequence single cells and to cultivate
three different species-level lineages of human oral Saccharibacteria/TM7. Using
our pure cultures we show that all three saccharibacteria species are epibionts
of diverse Actinobacteria. We also isolate and cultivate human
oral SR1 bacteria, which are members of a lineage of previously uncultured
bacteria. Reverse-genomics-enabled cultivation of microorganisms can be applied
to any species from any environment and has the potential to unlock the
isolation, cultivation and characterization of species from as-yet-uncultured
branches of the microbial tree of life.
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Affiliation(s)
- Karissa L Cross
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - James H Campbell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Natural Sciences, Northwest Missouri State University, Maryville, MO, USA
| | | | - Alisha G Campbell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology Program, University of Tennessee, Knoxville, TN, USA.,Department of Natural Sciences, Northwest Missouri State University, Maryville, MO, USA
| | - Sarah J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology Program, University of Tennessee, Knoxville, TN, USA
| | - Ann Griffen
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | | | - Snehal Joshi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dawn Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Eugene Leys
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Zamin Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology Program, University of Tennessee, Knoxville, TN, USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. .,Department of Microbiology, University of Tennessee, Knoxville, TN, USA. .,Genome Science and Technology Program, University of Tennessee, Knoxville, TN, USA.
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37
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Chen X, Wong CH, Ma C. Targeting the Bacterial Transglycosylase: Antibiotic Development from a Structural Perspective. ACS Infect Dis 2019; 5:1493-1504. [PMID: 31283163 DOI: 10.1021/acsinfecdis.9b00118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
One of the major threats to human life nowadays is widespread antibiotic resistance. Antibiotics are used to treat bacterial infections by targeting their essential pathways, such as the biosynthesis of bacterial cell walls. Bacterial transglycosylase, particularly glycosyltransferase family 51 (GT51), is one critical player in the cell wall biosynthesis and has long been known as a promising yet challenging target for antibiotic development. Here, we review the structural studies of this protein and summarize recent progress in developing its specific inhibitors, including synthetic substrate analogs and novel compounds identified from high-throughput screens. A detailed analysis of the protein-ligand interface has also provided us with valuable insights into the future antibiotic development against the bacterial transglycosylase.
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Affiliation(s)
- Xiaorui Chen
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
| | - Che Ma
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
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38
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Welsh MA, Schaefer K, Taguchi A, Kahne D, Walker S. Direction of Chain Growth and Substrate Preferences of Shape, Elongation, Division, and Sporulation-Family Peptidoglycan Glycosyltransferases. J Am Chem Soc 2019; 141:12994-12997. [PMID: 31386359 PMCID: PMC6738341 DOI: 10.1021/jacs.9b06358] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The bacterial cell wall is composed of peptidoglycan, and its biosynthesis is an established target for antibiotics. Peptidoglycan is assembled from a glycopeptide precursor, Lipid II, that is polymerized by peptidoglycan glycosyltransferases into glycan strands that are subsequently cross-linked to form the mature cell wall. For decades bacteria were thought to contain only one family of enzymes that polymerize Lipid II, but recently, the ubiquitous Shape, Elongation, Division, and Sporulation (SEDS)-family proteins RodA and FtsW were shown to be peptidoglycan polymerases. Because RodA and FtsW are essential in nearly all bacteria, these enzymes are promising targets for new antibiotics. However, almost nothing is known about the mechanisms of these polymerases. Here, we report that SEDS proteins synthesize peptidoglycan by adding new Lipid II monomers to the reducing end of the growing glycan chain. Using substrates that can only react at the reducing end, we also show that the glycosyl donor and acceptor in the polymerization reaction have distinct lipid requirements. These findings provide the first fundamental insights into the mechanism of SEDS-family polymerases and lay the groundwork for future biochemical and structural studies.
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Affiliation(s)
- Michael A. Welsh
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Kaitlin Schaefer
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Atsushi Taguchi
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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39
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Loos MS, Ramakrishnan R, Vranken W, Tsirigotaki A, Tsare EP, Zorzini V, Geyter JD, Yuan B, Tsamardinos I, Klappa M, Schymkowitz J, Rousseau F, Karamanou S, Economou A. Structural Basis of the Subcellular Topology Landscape of Escherichia coli. Front Microbiol 2019; 10:1670. [PMID: 31404336 PMCID: PMC6677119 DOI: 10.3389/fmicb.2019.01670] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Cellular proteomes are distributed in multiple compartments: on DNA, ribosomes, on and inside membranes, or they become secreted. Structural properties that allow polypeptides to occupy subcellular niches, particularly to after crossing membranes, remain unclear. We compared intrinsic and extrinsic features in cytoplasmic and secreted polypeptides of the Escherichia coli K-12 proteome. Structural features between the cytoplasmome and secretome are sharply distinct, such that a signal peptide-agnostic machine learning tool distinguishes cytoplasmic from secreted proteins with 95.5% success. Cytoplasmic polypeptides are enriched in aliphatic, aromatic, charged and hydrophobic residues, unique folds and higher early folding propensities. Secretory polypeptides are enriched in polar/small amino acids, β folds, have higher backbone dynamics, higher disorder and contact order and are more often intrinsically disordered. These non-random distributions and experimental evidence imply that evolutionary pressure selected enhanced secretome flexibility, slow folding and looser structures, placing the secretome in a distinct protein class. These adaptations protect the secretome from premature folding during its cytoplasmic transit, optimize its lipid bilayer crossing and allowed it to acquire cell envelope specific chemistries. The latter may favor promiscuous multi-ligand binding, sensing of stress and cell envelope structure changes. In conclusion, enhanced flexibility, slow folding, looser structures and unique folds differentiate the secretome from the cytoplasmome. These findings have wide implications on the structural diversity and evolution of modern proteomes and the protein folding problem.
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Affiliation(s)
- Maria S Loos
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Reshmi Ramakrishnan
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.,VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, Free University of Brussels, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel and Center for Structural Biology, Brussels, Belgium
| | - Alexandra Tsirigotaki
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Evrydiki-Pandora Tsare
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas, Patras, Greece
| | - Valentina Zorzini
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jozefien De Geyter
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Biao Yuan
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Ioannis Tsamardinos
- Gnosis Data Analysis PC, Heraklion, Greece.,Department of Computer Science, University of Crete, Heraklion, Greece
| | - Maria Klappa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas, Patras, Greece
| | - Joost Schymkowitz
- VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.,Gnosis Data Analysis PC, Heraklion, Greece
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40
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Yang H, Wang F, Wang H, Lu X, Shen W, Chen X. Deleting mrdA and mrcB to significantly improve extracellular recombinant protein production in Escherichia coli. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Maya-Martinez R, Alexander JAN, Otten CF, Ayala I, Vollmer D, Gray J, Bougault CM, Burt A, Laguri C, Fonvielle M, Arthur M, Strynadka NCJ, Vollmer W, Simorre JP. Recognition of Peptidoglycan Fragments by the Transpeptidase PBP4 From Staphylococcus aureus. Front Microbiol 2019; 9:3223. [PMID: 30713527 PMCID: PMC6346638 DOI: 10.3389/fmicb.2018.03223] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan (PG) is an essential component of the cell envelope, maintaining bacterial cell shape and protecting it from bursting due to turgor pressure. The monoderm bacterium Staphylococcus aureus has a highly cross-linked PG, with ~90% of peptide stems participating in DD-cross-links and up to 15 peptide stems connected with each other. These cross-links are formed in transpeptidation reactions catalyzed by penicillin-binding proteins (PBPs) of classes A and B. Most S. aureus strains have three housekeeping PBPs with this function (PBP1, PBP2, and PBP3) but MRSA strains have acquired a third class B PBP, PBP2a, which is encoded by the mecA gene and required for the expression of high-level resistance to β-lactams. Another housekeeping PBP of S. aureus is PBP4, which belongs to the class C PBPs, and hence would be expected to have PG hydrolase (DD-carboxypeptidase or DD-endopeptidase) activity. However, previous works showed that, unexpectedly, PBP4 has transpeptidase activity that significantly contributes to both the high level of cross-linking in the PG of S. aureus and to the low level of β-lactam resistance in the absence of PBP2a. To gain insights into this unusual activity of PBP4, we studied by NMR spectroscopy its interaction in vitro with different substrates, including intact peptidoglycan, synthetic peptide stems, muropeptides, and long glycan chains with uncross-linked peptide stems. PBP4 showed no affinity for the complex, intact peptidoglycan or the smallest isolated peptide stems. Transpeptidase activity of PBP4 was verified with the disaccharide peptide subunits (muropeptides) in vitro, producing cyclic dimer and multimer products; these assays also showed a designed PBP4(S75C) nucleophile mutant to be inactive. Using this inactive but structurally highly similar variant, liquid-state NMR identified two interaction surfaces in close proximity to the central nucleophile position that can accommodate the potential donor and acceptor stems for the transpeptidation reaction. A PBP4:muropeptide model structure was built from these experimental restraints, which provides new mechanistic insights into mecA independent resistance to β-lactams in S. aureus.
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Affiliation(s)
| | - J Andrew N Alexander
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Christian F Otten
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Isabel Ayala
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Daniela Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joe Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Alister Burt
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Cédric Laguri
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Matthieu Fonvielle
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Université Sorbone-Paris, Paris, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Université Sorbone-Paris, Paris, France
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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42
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Miyachiro MM, Contreras-Martel C, Dessen A. Penicillin-Binding Proteins (PBPs) and Bacterial Cell Wall Elongation Complexes. Subcell Biochem 2019; 93:273-289. [PMID: 31939154 DOI: 10.1007/978-3-030-28151-9_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bacterial cell wall is the validated target of mainstream antimicrobials such as penicillin and vancomycin. Penicillin and other β-lactams act by targeting Penicillin-Binding Proteins (PBPs), enzymes that play key roles in the biosynthesis of the main component of the cell wall, the peptidoglycan. Despite the spread of resistance towards these drugs, the bacterial cell wall continues to be a major Achilles' heel for microbial survival, and the exploration of the cell wall formation machinery is a vast field of work that can lead to the development of novel exciting therapies. The sheer complexity of the cell wall formation process, however, has created a significant challenge for the study of the macromolecular interactions that regulate peptidoglycan biosynthesis. New developments in genetic and biochemical screens, as well as different aspects of structural biology, have shed new light on the importance of complexes formed by PBPs, notably within the cell wall elongation machinery. This chapter summarizes structural and functional details of PBP complexes involved in the periplasmic and membrane steps of peptidoglycan biosynthesis with a focus on cell wall elongation. These assemblies could represent interesting new targets for the eventual development of original antibacterials.
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Affiliation(s)
- Mayara M Miyachiro
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, Brazil
| | - Carlos Contreras-Martel
- Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, Grenoble, France
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, Brazil. .,Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, Grenoble, France.
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43
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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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44
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Egan AJF, Maya-Martinez R, Ayala I, Bougault CM, Banzhaf M, Breukink E, Vollmer W, Simorre JP. Induced conformational changes activate the peptidoglycan synthase PBP1B. Mol Microbiol 2018; 110:335-356. [PMID: 30044025 PMCID: PMC6220978 DOI: 10.1111/mmi.14082] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2018] [Indexed: 12/25/2022]
Abstract
Bacteria surround their cytoplasmic membrane with an essential, stress‐bearing peptidoglycan (PG) layer consisting of glycan chains linked by short peptides into a mesh‐like structure. Growing and dividing cells expand their PG layer using inner‐membrane anchored PG synthases, including Penicillin‐binding proteins (PBPs), which participate in dynamic protein complexes to facilitate cell wall growth. In Escherichia coli, and presumably other Gram‐negative bacteria, growth of the mainly single layered PG is regulated by outer membrane‐anchored lipoproteins. The lipoprotein LpoB is required to activate PBP1B, which is a major, bi‐functional PG synthase with glycan chain polymerising (glycosyltransferase) and peptide cross‐linking (transpeptidase) activities. In this work we show how the binding of LpoB to the regulatory UB2H domain of PBP1B activates both activities. Binding induces structural changes in the UB2H domain, which transduce to the two catalytic domains by distinct allosteric pathways. We also show how an additional regulator protein, CpoB, is able to selectively modulate the TPase activation by LpoB without interfering with GTase activation.
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Affiliation(s)
- Alexander J F Egan
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Roberto Maya-Martinez
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71 avenue des Martyrs, 38000, Grenoble, France
| | - Isabel Ayala
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71 avenue des Martyrs, 38000, Grenoble, France
| | - Catherine M Bougault
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71 avenue des Martyrs, 38000, Grenoble, France
| | - Manuel Banzhaf
- European Molecular Biology Laboratory Heidelberg, Genome Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.,Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham , B15 2TT, UK
| | - Eefjan Breukink
- Bijvoet Center for Biomolecular Research, Department of Biochemistry of Membranes, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71 avenue des Martyrs, 38000, Grenoble, France
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45
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Crépin S, Ottosen EN, Peters K, Smith SN, Himpsl SD, Vollmer W, Mobley HLT. The lytic transglycosylase MltB connects membrane homeostasis and in vivo fitness of Acinetobacter baumannii. Mol Microbiol 2018; 109:745-762. [PMID: 29884996 PMCID: PMC6185781 DOI: 10.1111/mmi.14000] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/30/2018] [Accepted: 07/15/2018] [Indexed: 01/06/2023]
Abstract
Acinetobacter baumannii has emerged as a leading nosocomial pathogen, infecting a wide range of anatomic sites including the respiratory tract and the bloodstream. In addition to being multi‐drug resistant, little is known about the molecular basis of A. baumannii pathogenesis. To better understand A. baumannii virulence, a combination of a transposon‐sequencing (TraDIS) screen and the neutropenic mouse model of bacteremia was used to identify the full set of fitness genes required during bloodstream infection. The lytic transglycosylase MltB was identified as a critical fitness factor. MltB cleaves the MurNAc‐GlcNAc bond of peptidoglycan, which leads to cell wall remodeling. Here we show that MltB is part of a complex network connecting resistance to stresses, membrane homeostasis, biogenesis of pili and in vivo fitness. Indeed, inactivation of mltB not only impaired resistance to serum complement, cationic antimicrobial peptides and oxygen species, but also altered the cell envelope integrity, activated the envelope stress response, drastically reduced the number of pili at the cell surface and finally, significantly decreased colonization of both the bloodstream and the respiratory tract.
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Affiliation(s)
- Sébastien Crépin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Elizabeth N Ottosen
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sara N Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephanie D Himpsl
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Harry L T Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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46
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Abstract
Monoamine oxidases A and B (MAO A and B) are mammalian flavoenzymes bound to the outer mitochondrial membrane. They were discovered almost a century ago and they have been the subject of many biochemical, structural and pharmacological investigations due to their central role in neurotransmitter metabolism. Currently, the treatment of Parkinson's disease involves the use of selective MAO B inhibitors such as rasagiline and safinamide. MAO inhibition was shown to exert a general neuroprotective effect as a result of the reduction of oxidative stress produced by these enzymes, which seems to be relevant also in non-neuronal contexts. MAOs were successfully expressed as recombinant proteins in Pichia pastoris, which allowed a thorough biochemical and structural characterization. These enzymes are characterized by a globular water-soluble main body that is anchored to the mitochondrial membrane through a C-terminal α-helix, similar to other bitopic membrane proteins. In both MAO A and MAO B the enzyme active site consists of a hydrophobic cavity lined by residues that are conserved in the two isozymes, except for few details that determine substrate and inhibitor specificity. In particular, human MAO B features a dual-cavity active site whose conformation depends on the size of the bound ligand. This article provides a comprehensive and historical review of MAOs and the state-of-the-art of these enzymes as membrane drug targets.
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Affiliation(s)
| | - Claudia Binda
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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47
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Dik DA, Fisher JF, Mobashery S. Cell-Wall Recycling of the Gram-Negative Bacteria and the Nexus to Antibiotic Resistance. Chem Rev 2018; 118:5952-5984. [PMID: 29847102 PMCID: PMC6855303 DOI: 10.1021/acs.chemrev.8b00277] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The importance of the cell wall to the viability of the bacterium is underscored by the breadth of antibiotic structures that act by blocking key enzymes that are tasked with cell-wall creation, preservation, and regulation. The interplay between cell-wall integrity, and the summoning forth of resistance mechanisms to deactivate cell-wall-targeting antibiotics, involves exquisite orchestration among cell-wall synthesis and remodeling and the detection of and response to the antibiotics through modulation of gene regulation by specific effectors. Given the profound importance of antibiotics to the practice of medicine, the assertion that understanding this interplay is among the most fundamentally important questions in bacterial physiology is credible. The enigmatic regulation of the expression of the AmpC β-lactamase, a clinically significant and highly regulated resistance response of certain Gram-negative bacteria to the β-lactam antibiotics, is the exemplar of this challenge. This review gives a current perspective to this compelling, and still not fully solved, 35-year enigma.
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Affiliation(s)
- David A. Dik
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jed F. Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
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48
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Dahmane I, Montagner C, Matagne A, Dumbre S, Herdewijn P, Terrak M. Peptidoglycan glycosyltransferase-ligand binding assay based on tryptophan fluorescence quenching. Biochimie 2018; 152:1-5. [PMID: 29909047 DOI: 10.1016/j.biochi.2018.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/13/2018] [Indexed: 11/28/2022]
Abstract
Peptidoglycan glycosyltransferases (GTase) of family 51 are essential enzymes for the synthesis of the glycan chains of the bacterial cell wall. They are considered potential antibacterial target, but discovery of inhibitors was hampered so far by the lack of efficient and affordable screening assay. Here we used Staphylococcus aureus MtgA to introduce a single tryptophan reporter residue in selected positions flanking the substrates binding cavity of the protein. We selected a mutant (Y181W) that shows strong fluorescence quenching in the presence of moenomycin A and two lipid II analogs inhibitors. The assay provides a simple method to study GTase-ligand interactions and can be used as primary high throughput screening of GTase inhibitors without the need for lipid II substrate or reporter ligands.
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Affiliation(s)
- Ismahene Dahmane
- Centre d'Ingénierie des Protéines-InBioS, University of Liège, B6a, Quartier Agora, Allée du six Août 11, 4000, Liège 1, Belgium
| | - Caroline Montagner
- Centre d'Ingénierie des Protéines-InBioS, University of Liège, B6a, Quartier Agora, Allée du six Août 11, 4000, Liège 1, Belgium
| | - André Matagne
- Centre d'Ingénierie des Protéines-InBioS, University of Liège, B6a, Quartier Agora, Allée du six Août 11, 4000, Liège 1, Belgium
| | - Shrinivas Dumbre
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Belgium
| | - Mohammed Terrak
- Centre d'Ingénierie des Protéines-InBioS, University of Liège, B6a, Quartier Agora, Allée du six Août 11, 4000, Liège 1, Belgium.
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49
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Caveney NA, Li FK, Strynadka NC. Enzyme structures of the bacterial peptidoglycan and wall teichoic acid biogenesis pathways. Curr Opin Struct Biol 2018; 53:45-58. [PMID: 29885610 DOI: 10.1016/j.sbi.2018.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/08/2018] [Accepted: 05/16/2018] [Indexed: 01/08/2023]
Abstract
The bacterial cell wall is a complex polymeric structure with essential roles in defence, survival and pathogenesis. Common to both Gram-positive and Gram-negative bacteria is the mesh-like peptidoglycan sacculus that surrounds the outer leaflet of the cytoplasmic membrane. Recent crystallographic studies of enzymes that comprise the peptidoglycan biosynthetic pathway have led to significant new understanding of all stages. These include initial multi-step cytosolic formation of sugar-pentapeptide precursors, transfer of the precursors to activated polyprenyl lipids at the membrane inner leaflet and flippase mediated relocalization of the resulting lipid II precursors to the outer leaflet where glycopolymerization and subsequent peptide crosslinking are finalized. Additional, species-specific enzymes allow customized peptidoglycan modifications and biosynthetic regulation that are important to bacterial virulence and survival. These studies have reinforced the unique and specific catalytic mechanisms at play in cell wall biogenesis and expanded the atomic foundation to develop novel, structure guided, antibacterial agents.
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Affiliation(s)
- Nathanael A Caveney
- University of British Columbia, Biochemistry and Molecular Biology and the Center for Blood Research, Rm 4350 Life Sciences Center, 2350 Health Sciences Mall, Vancouver V6T 1Z3 Canada
| | - Franco Kk Li
- University of British Columbia, Biochemistry and Molecular Biology and the Center for Blood Research, Rm 4350 Life Sciences Center, 2350 Health Sciences Mall, Vancouver V6T 1Z3 Canada
| | - Natalie Cj Strynadka
- University of British Columbia, Biochemistry and Molecular Biology and the Center for Blood Research, Rm 4350 Life Sciences Center, 2350 Health Sciences Mall, Vancouver V6T 1Z3 Canada.
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50
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Punekar AS, Samsudin F, Lloyd AJ, Dowson CG, Scott DJ, Khalid S, Roper DI. The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization. Cell Surf 2018; 2:54-66. [PMID: 30046666 PMCID: PMC6053601 DOI: 10.1016/j.tcsw.2018.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/27/2022] Open
Abstract
Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the essential polymerization of lipid II into linear glycan chains required for peptidoglycan biosynthesis. The PGT domain is composed of a large head subdomain and a smaller jaw subdomain and can be potently inhibited by the antibiotic moenomycin A (MoeA). We present an X-ray structure of the MoeA-bound Staphylococcus aureus monofunctional PGT enzyme, revealing electron density for a second MoeA bound to the jaw subdomain as well as the PGT donor site. Isothermal titration calorimetry confirms two drug-binding sites with markedly different affinities and positive cooperativity. Hydrophobic cluster analysis suggests that the membrane-interacting surface of the jaw subdomain has structural and physicochemical properties similar to amphipathic cationic α -helical antimicrobial peptides for lipid II recognition and binding. Furthermore, molecular dynamics simulations of the drug-free and -bound forms of the enzyme demonstrate the importance of the jaw subdomain movement for lipid II selection and polymerization process and provide molecular-level insights into the mechanism of peptidoglycan biosynthesis by PGTs.
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Affiliation(s)
- Avinash S. Punekar
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Adrian J. Lloyd
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - David J. Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
- ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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