101
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Ameryckx A, Thabault L, Pochet L, Leimanis S, Poupaert JH, Wouters J, Joris B, Van Bambeke F, Frédérick R. 1-(2-Hydroxybenzoyl)-thiosemicarbazides are promising antimicrobial agents targeting d-alanine-d-alanine ligase in bacterio. Eur J Med Chem 2018; 159:324-338. [DOI: 10.1016/j.ejmech.2018.09.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/09/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
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102
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Alexander JAN, Chatterjee SS, Hamilton SM, Eltis LD, Chambers HF, Strynadka NCJ. Structural and kinetic analyses of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance in Staphylococcus aureus. J Biol Chem 2018; 293:19854-19865. [PMID: 30366985 DOI: 10.1074/jbc.ra118.004952] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/24/2018] [Indexed: 01/08/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) causes serious community-acquired and nosocomial infections worldwide. MRSA strains are resistant to a variety of antibiotics, including the classic penicillin and cephalosporin classes of β-lactams, making them intractable to treatment. Although β-lactam resistance in MRSA has been ascribed to the acquisition and activity of penicillin-binding protein 2a (PBP2a, encoded by mecA), it has recently been observed that resistance can also be mediated by penicillin-binding protein 4 (PBP4). Previously, we have shown that broad-spectrum β-lactam resistance can arise following serial passaging of a mecA-negative COL strain of S. aureus, creating the CRB strain. This strain has two missense mutations in pbp4 and a mutation in the pbp4 promoter, both of which play an instrumental role in β-lactam resistance. To better understand PBP4's role in resistance, here we have characterized its kinetics and structure with clinically relevant β-lactam antibiotics. We present the first crystallographic PBP4 structures of apo and acyl-enzyme intermediate forms complexed with three late-generation β-lactam antibiotics: ceftobiprole, ceftaroline, and nafcillin. In parallel, we characterized the structural and kinetic effects of the PBP4 mutations present in the CRB strain. Localized within the transpeptidase active-site cleft, the two substitutions appear to have different effects depending on the drug. With ceftobiprole, the missense mutations impaired the Km value 150-fold, decreasing the proportion of inhibited PBP4. However, ceftaroline resistance appeared to be mediated by other factors, possibly including mutation of the pbp4 promoter. Our findings provide evidence that S. aureus CRB has at least two PBP4-mediated resistance mechanisms.
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Affiliation(s)
- J Andrew N Alexander
- From the Department of Biochemistry and Molecular Biology.,the Centre for Blood Research, and
| | - Som S Chatterjee
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Stephanie M Hamilton
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Lindsay D Eltis
- From the Department of Biochemistry and Molecular Biology.,the Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and
| | - Henry F Chambers
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Natalie C J Strynadka
- From the Department of Biochemistry and Molecular Biology, .,the Centre for Blood Research, and
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103
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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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104
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Kemung HM, Tan LTH, Khan TM, Chan KG, Pusparajah P, Goh BH, Lee LH. Streptomyces as a Prominent Resource of Future Anti-MRSA Drugs. Front Microbiol 2018; 9:2221. [PMID: 30319563 PMCID: PMC6165876 DOI: 10.3389/fmicb.2018.02221] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/30/2018] [Indexed: 01/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) pose a significant health threat as they tend to cause severe infections in vulnerable populations and are difficult to treat due to a limited range of effective antibiotics and also their ability to form biofilm. These organisms were once limited to hospital acquired infections but are now widely present in the community and even in animals. Furthermore, these organisms are constantly evolving to develop resistance to more antibiotics. This results in a need for new clinically useful antibiotics and one potential source are the Streptomyces which have already been the source of several anti-MRSA drugs including vancomycin. There remain large numbers of Streptomyces potentially undiscovered in underexplored regions such as mangrove, deserts, marine, and freshwater environments as well as endophytes. Organisms from these regions also face significant challenges to survival which often result in the production of novel bioactive compounds, several of which have already shown promise in drug development. We review the various mechanisms of antibiotic resistance in MRSA and all the known compounds isolated from Streptomyces with anti-MRSA activity with a focus on those from underexplored regions. The isolation of the full array of compounds Streptomyces are potentially capable of producing in the laboratory has proven a challenge, we also review techniques that have been used to overcome this obstacle including genetic cluster analysis. Additionally, we review the in vivo work done thus far with promising compounds of Streptomyces origin as well as the animal models that could be used for this work.
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Affiliation(s)
- Hefa Mangzira Kemung
- Novel Bacteria and Drug Discovery Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,Biofunctional Molecule Exploratory Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Loh Teng-Hern Tan
- Novel Bacteria and Drug Discovery Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,Biofunctional Molecule Exploratory Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Tahir Mehmood Khan
- Novel Bacteria and Drug Discovery Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,Biofunctional Molecule Exploratory Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,The Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore, Pakistan
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,International Genome Centre, Jiangsu University, Zhenjiang, China
| | - Priyia Pusparajah
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Bey-Hing Goh
- Novel Bacteria and Drug Discovery Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,Biofunctional Molecule Exploratory Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Mueang Phayao, Thailand
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,Biofunctional Molecule Exploratory Research Group, Biomedicine Research Advancement Centre, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia.,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia.,Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Mueang Phayao, Thailand
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105
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Tibaut T, Tomašič T, Hodnik V, Anderluh M, Pintar S, Novič M, Turk D. Application of fragment based virtual screening towards inhibition of bacterial N-acetyglucosaminidase $. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:647-660. [PMID: 30160524 DOI: 10.1080/1062936x.2018.1504116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
A structure-based approach is applied for the development of inhibitors of bacterial N-acetyglucosaminidase (autolysin). Autolysins are enzymes involved in the degradation of peptidoglycan and therefore participate in bacterial cell growth and different lysis phenomena. Several studies indicate that by the inhibition of autolysins, and consequently of bacterial cell division, antibacterial activity can be obtained, thus paving the road to a novel group of therapeutics against human pathogens. As crystal structures of the autolysin E (AtlE)-ligand complexes were obtained in our laboratories, fragment-based virtual screening was the method of choice for the initial studies. Fragment libraries from various databases were merged to increase the number of compounds for the virtual screening. Twenty-four commercially available virtual hits were selected and subjected to quantitative analysis of binding interactions using the surface plasmon resonance technique. Twelve fragments showed fragment-AtlE interactions. For F1, the top hit of the virtual screening, a KD of 228 µM was determined, while other fragments displayed non-stoichiometric binding. Blind docking of potential binders uncovers three possible allosteric sites. Ligands of N-acetyglucosaminidase identified in our study represent valuable information for the further development of AtlE inhibitors, which could in future represent antibacterial agents acting by a novel mode of action.
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Affiliation(s)
- T Tibaut
- a Theory Department, Laboratory for Chemometrics , National Institute of Chemistry , Ljubljana, Slovenia
- b Chair of Pharmaceutical Chemistry, Faculty of Pharmacy , University of Ljubljana , Ljubljana, Slovenia
| | - T Tomašič
- b Chair of Pharmaceutical Chemistry, Faculty of Pharmacy , University of Ljubljana , Ljubljana, Slovenia
| | - V Hodnik
- c Department of Biology, Biotechnical Faculty , University of Ljubljana , Ljubljana, Slovenia
| | - M Anderluh
- b Chair of Pharmaceutical Chemistry, Faculty of Pharmacy , University of Ljubljana , Ljubljana, Slovenia
| | - S Pintar
- d Department of Biochemistry and Molecular and Structural Biology , Jozef Stefan Institute , Ljubljana, Slovenia
| | - M Novič
- a Theory Department, Laboratory for Chemometrics , National Institute of Chemistry , Ljubljana, Slovenia
| | - D Turk
- d Department of Biochemistry and Molecular and Structural Biology , Jozef Stefan Institute , Ljubljana, Slovenia
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106
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Wang X, Krasnova L, Wu KB, Wu WS, Cheng TJ, Wong CH. Towards new antibiotics targeting bacterial transglycosylase: Synthesis of a Lipid II analog as stable transition-state mimic inhibitor. Bioorg Med Chem Lett 2018; 28:2708-2712. [PMID: 29602680 PMCID: PMC6182773 DOI: 10.1016/j.bmcl.2018.03.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
Abstract
Described here is the asymmetric synthesis of iminosugar 2b, a Lipid II analog, designed to mimic the transition state of transglycosylation catalyzed by the bacterial transglycosylase. The high density of functional groups, together with a rich stereochemistry, represents an extraordinary challenge for chemical synthesis. The key 2,6-anti- stereochemistry of the iminosugar ring was established through an iridium-catalyzed asymmetric allylic amination. The developed synthetic route is suitable for the synthesis of focused libraries to enable the structure-activity relationship study and late-stage modification of iminosugar scaffold with variable lipid, peptide and sugar substituents. Compound 2b showed 70% inhibition of transglycosylase from Acinetobacter baumannii, providing a basis for further improvement.
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Affiliation(s)
- Xiaolei Wang
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Larissa Krasnova
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Kevin Binchia Wu
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Wei-Shen Wu
- Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan
| | - Ting-Jen Cheng
- Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan
| | - Chi-Huey Wong
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA; Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan.
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107
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Evidence for substrate-assisted catalysis in N-acetylphosphoglucosamine mutase. Biochem J 2018; 475:2547-2557. [PMID: 29967067 PMCID: PMC6096347 DOI: 10.1042/bcj20180172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 11/17/2022]
Abstract
N-acetylphosphoglucosamine mutase (AGM1) is a key component of the hexosamine biosynthetic pathway that produces UDP-GlcNAc, an essential precursor for a wide range of glycans in eukaryotes. AGM belongs to the α-d-phosphohexomutase metalloenzyme superfamily and catalyzes the interconversion of N-acetylglucosamine-6-phosphate (GlcNAc-6P) to N-acetylglucosamine-1-phosphate (GlcNAc-1P) through N-acetylglucosamine-1,6-bisphosphate (GlcNAc-1,6-bisP) as the catalytic intermediate. Although there is an understanding of the phosphoserine-dependent catalytic mechanism at enzymatic and structural level, the identity of the requisite catalytic base in AGM1/phosphoglucomutases is as yet unknown. Here, we present crystal structures of a Michaelis complex of AGM1 with GlcNAc-6P and Mg2+, and a complex of the inactive Ser69Ala mutant together with glucose-1,6-bisphosphate (Glc-1,6-bisP) that represents key snapshots along the reaction co-ordinate. Together with mutagenesis, these structures reveal that the phosphate group of the hexose-1,6-bisP intermediate may act as the catalytic base.
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108
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Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
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109
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Romaniuk JAH, Cegelski L. Peptidoglycan and Teichoic Acid Levels and Alterations in Staphylococcus aureus by Cell-Wall and Whole-Cell Nuclear Magnetic Resonance. Biochemistry 2018; 57:3966-3975. [PMID: 29806458 PMCID: PMC6309457 DOI: 10.1021/acs.biochem.8b00495] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gram-positive bacteria surround themselves with a multilayered macromolecular cell wall that is essential to cell survival and serves as a major target for antibiotics. The cell wall of Staphylococcus aureus is composed of two major structural components, peptidoglycan (PG) and wall teichoic acid (WTA), together creating a heterogeneous and insoluble matrix that poses a challenge to quantitative compositional analysis. Here, we present 13C cross polarization magic angle spinning solid-state nuclear magnetic resonance (NMR) spectra of intact cell walls, purified PG, and purified WTA. The spectra reveal the clear molecular differences in the two polymers and enable quantification of PG and WTA in isolated cell walls, an attractive alternative to estimating teichoic acid content from a phosphate analysis of completely pyrolyzed cell walls. Furthermore, we discovered that unique PG and WTA spectral signatures could be identified in whole-cell NMR spectra and used to compare PG and WTA levels among intact bacterial cell samples. The distinguishing whole-cell 13C NMR contributions associated with PG include the GlcNAc-MurNAc sugar carbons and glycyl α-carbons. WTA contributes carbons from the phosphoribitol backbone. Distinguishing 15N spectral signatures include glycyl amide nitrogens in PG and the esterified d-alanyl amine nitrogens in WTA. 13C NMR analysis was performed with samples at natural abundance and included 10 whole-cell sample comparisons. Changes consistent with altered PG and WTA content were detected in whole-cell spectra of bacteria harvested at different growth times and in cells treated with tunicamycin. This use of whole-cell NMR provides quantitative parameters of composition in the context of whole-cell activity.
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Affiliation(s)
| | - Lynette Cegelski
- Stanford University, Department of Chemistry, 380 Roth Way, Stanford CA 94305
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110
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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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111
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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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112
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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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113
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New use for CETSA: monitoring innate immune receptor stability via post-translational modification by OGT. J Bioenerg Biomembr 2018; 50:231-240. [PMID: 29671171 DOI: 10.1007/s10863-018-9754-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/21/2018] [Indexed: 01/01/2023]
Abstract
O-GlcNAcylation is a dynamic and functionally diverse post-translational modification shown to affect thousands of proteins, including the innate immune receptor nucleotide-binding oligomerization domain-containing protein 2 (Nod2). Mutations of Nod2 (R702W, G908R and 1007 fs) are associated with Crohn's disease and have lower stabilities compared to wild type. Cycloheximide (CHX)-chase half-life assays have been used to show that O-GlcNAcylation increases the stability and response of both wild type and Crohn's variant Nod2, R702W. A more rapid method to assess stability afforded by post-translational modifications is necessary to fully comprehend the correlation between NLR stability and O-GlcNAcylation. Here, a recently developed cellular thermal shift assay (CETSA) that is typically used to demonstrate protein-ligand binding was adapted to detect shifts in protein stabilization upon increasing O-GlcNAcylation levels in Nod2. This assay was used as a method to predict if other Crohn's associated Nod2 variants were O-GlcNAcylated, and also identified the modification on another NLR, Nod1. Classical immunoprecipitations and NF-κB transcriptional assays were used to confirm the presence and effect of this modification on these proteins. The results presented here demonstrate that CETSA is a convenient method that can be used to detect the stability effect of O-GlcNAcylation on O-GlcNAc-transferase (OGT) client proteins and will be a powerful tool in studying post-translational modification.
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114
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Rubino FA, Kumar S, Ruiz N, Walker S, Kahne DE. Membrane Potential Is Required for MurJ Function. J Am Chem Soc 2018; 140:4481-4484. [PMID: 29558128 DOI: 10.1021/jacs.8b00942] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MurJ, the flippase that exports the bacterial cell wall monomer Lipid II to the periplasm, is a target for new antibiotics, which are desperately needed to treat Gram-negative infections. Quantitative methods to monitor MurJ activity are required to characterize inhibitors but are challenging to develop because the lipid-linked substrate is not chemically altered in a flippase reaction. Here we show that MurJ inhibition can be quantified by measuring the accumulation of intracellular Lipid II using a biotin-tagging strategy. We have exploited this assay to show that MurJ is inhibited in the presence of a compound that dissipates the membrane potential. By probing cysteine accessibility we have found that under this condition MurJ relaxes into an inactive, outward-facing conformation reminiscent of that targeted by the peptide antibiotic LysM. We conclude that membrane potential is required for MurJ function in E. coli, and we anticipate that the ability to accumulate this inactive conformation will lead to structures useful for inhibitor design.
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Affiliation(s)
- Frederick A Rubino
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Sujeet Kumar
- Department of Microbiology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Natividad Ruiz
- Department of Microbiology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Daniel E Kahne
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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115
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Palzkill T. Structural and Mechanistic Basis for Extended-Spectrum Drug-Resistance Mutations in Altering the Specificity of TEM, CTX-M, and KPC β-lactamases. Front Mol Biosci 2018; 5:16. [PMID: 29527530 PMCID: PMC5829062 DOI: 10.3389/fmolb.2018.00016] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/08/2018] [Indexed: 11/13/2022] Open
Abstract
The most common mechanism of resistance to β-lactam antibiotics in Gram-negative bacteria is the production of β-lactamases that hydrolyze the drugs. Class A β-lactamases are serine active-site hydrolases that include the common TEM, CTX-M, and KPC enzymes. The TEM enzymes readily hydrolyze penicillins and older cephalosporins. Oxyimino-cephalosporins, such as cefotaxime and ceftazidime, however, are poor substrates for TEM-1 and were introduced, in part, to circumvent β-lactamase-mediated resistance. Nevertheless, the use of these antibiotics has lead to evolution of numerous variants of TEM with mutations that significantly increase the hydrolysis of the newer cephalosporins. The CTX-M enzymes emerged in the late 1980s and hydrolyze penicillins and older cephalosporins and derive their name from the ability to also hydrolyze cefotaxime. The CTX-M enzymes, however, do not efficiently hydrolyze ceftazidime. Variants of CTX-M enzymes, however, have evolved that exhibit increased hydrolysis of ceftazidime. Finally, the KPC enzyme emerged in the 1990s and is characterized by its broad specificity that includes penicillins, most cephalosporins, and carbapenems. The KPC enzyme, however, does not efficiently hydrolyze ceftazidime. As with the TEM and CTX-M enzymes, variants have recently evolved that extend the spectrum of KPC β-lactamase to include ceftazidime. This review discusses the structural and mechanistic basis for the expanded substrate specificity of each of these enzymes that result from natural mutations that confer oxyimino-cephalosporin resistance. For the TEM enzyme, extended-spectrum mutations act by establishing new interactions with the cephalosporin. These mutations increase the conformational heterogeneity of the active site to create sub-states that better accommodate the larger drugs. The mutations expanding the spectrum of CTX-M enzymes also affect the flexibility and conformation of the active site to accommodate ceftazidime. Although structural data are limited, extended-spectrum mutations in KPC may act by mediating new, direct interactions with substrate and/or altering conformations of the active site. In many cases, mutations that expand the substrate profile of these enzymes simultaneously decrease the thermodynamic stability. This leads to the emergence of additional global suppressor mutations that help correct the stability defects leading to increased protein expression and increased antibiotic resistance.
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Affiliation(s)
- Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States
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116
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Kawai Y, Mickiewicz K, Errington J. Lysozyme Counteracts β-Lactam Antibiotics by Promoting the Emergence of L-Form Bacteria. Cell 2018; 172:1038-1049.e10. [PMID: 29456081 PMCID: PMC5847170 DOI: 10.1016/j.cell.2018.01.021] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 11/13/2017] [Accepted: 01/12/2018] [Indexed: 01/01/2023]
Abstract
β-lactam antibiotics inhibit bacterial cell wall assembly and, under classical microbiological culture conditions that are generally hypotonic, induce explosive cell death. Here, we show that under more physiological, osmoprotective conditions, for various Gram-positive bacteria, lysis is delayed or abolished, apparently because inhibition of class A penicillin-binding protein leads to a block in autolytic activity. Although these cells still then die by other mechanisms, exogenous lytic enzymes, such as lysozyme, can rescue viability by enabling the escape of cell wall-deficient "L-form" bacteria. This protective L-form conversion was also observed in macrophages and in an animal model, presumably due to the production of host lytic activities, including lysozyme. Our results demonstrate the potential for L-form switching in the host environment and highlight the unexpected effects of innate immune effectors, such as lysozyme, on antibiotic activity. Unlike previously described dormant persisters, L-forms can continue to proliferate in the presence of antibiotic.
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Affiliation(s)
- Yoshikazu Kawai
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Katarzyna Mickiewicz
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK.
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117
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Ruscitto A, Sharma A. Peptidoglycan synthesis in Tannerella forsythia: Scavenging is the modus operandi. Mol Oral Microbiol 2018; 33:125-132. [PMID: 29247483 DOI: 10.1111/omi.12210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2017] [Indexed: 01/05/2023]
Abstract
Tannerella forsythia is a Gram-negative oral pathogen strongly associated with periodontitis. This bacterium has an absolute requirement for exogenous N-acetylmuramic acid (MurNAc), an amino sugar that forms the repeating disaccharide unit with amino sugar N-acetylglucosamine (GlcNAc) of the peptidoglycan backbone. In silico genome analysis indicates that T. forsythia lacks the key biosynthetic enzymes needed for the de novo synthesis of MurNAc, and so relies on alternative ways to meet its requirement for peptidoglycan biosynthesis. In the subgingival niche, the bacterium can acquire MurNAc and peptidoglycan fragments (muropeptides) released by the cohabiting bacteria during their cell wall breakdown associated with cell division. Tannerella forsythia is able to also use host sialic acid (Neu5Ac) in lieu of MurNAc or muropeptides for its survival during the biofilm growth. Evidence suggests that the bacterium might be able to shunt sialic acid into a metabolic pathway leading to peptidoglycan synthesis. In this review, we explore the mechanisms by which T. forsythia is able to scavenge MurNAc, muropeptide and sialic acid for its peptidoglycan synthesis, and the impact of these scavenging activities on pathogenesis.
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Affiliation(s)
| | - A Sharma
- Department of Oral Biology, University at Buffalo, Buffalo, NY, USA
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118
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Asai K. Anti-sigma factor-mediated cell surface stress responses in Bacillus subtilis. Genes Genet Syst 2018; 92:223-234. [PMID: 29343670 DOI: 10.1266/ggs.17-00046] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Proteins belonging to the sigma factor family in eubacteria initiate transcription by associating with RNA polymerase. A subfamily, the extracytoplasmic function (ECF) sigma factors, which form a widely distributed bacterial signal transduction system comprising a sigma factor and a cognate membrane-embedded anti-sigma factor, regulates genes in response to stressors that threaten cell envelope integrity including the cell wall and membrane. The Gram-positive soil bacterium Bacillus subtilis provides a valuable model for investigation of the ECF sigma factors. This review focuses on the function and regulation of ECF sigma factors in B. subtilis, in which anti-sigma factors play a role in connecting an external stimulus with gene regulation. As representative examples, the regulon and regulatory mechanism of σW are closely associated with membrane-active stressors, whereas σM is strongly induced by conditions that impair peptidoglycan synthesis. These studies demonstrate that the mechanisms of ECF-dependent signaling are divergent and constitute a multi-layered hierarchy, and provide useful insights into the elucidation of unknown mechanisms related to ECF sigma factors.
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Affiliation(s)
- Kei Asai
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture
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119
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Salmon-Divon M, Yeheskel A, Kornspan D. Genomic analysis of the original Elberg Brucella melitensis Rev.1 vaccine strain reveals insights into virulence attenuation. Virulence 2018; 9:1436-1448. [PMID: 30139304 PMCID: PMC6141144 DOI: 10.1080/21505594.2018.1511677] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 11/30/2022] Open
Abstract
The live attenuated Brucella melitensis Rev.1 Elberg-originated vaccine strain has been widely used to control brucellosis in small ruminants. However, despite extensive research, the molecular mechanisms underlying the attenuation of this strain are still unknown. In the current study, we conducted a comprehensive comparative analysis of the whole-genome sequence of Rev.1 against that of the virulent reference strain, B. melitensis 16M. This analysis revealed five regions of insertion and three regions of deletion within the Rev.1 genome, among which, one large region of insertion, comprising 3,951 bp, was detected in the Rev.1 genome. In addition, we found several missense mutations within important virulence-related genes, which may be used to determine the mechanism underlying virulence attenuation. Collectively, our findings provide new insights into the Brucella virulence mechanisms and, therefore, may serve as a basis for the rational design of new Brucella vaccines.
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Affiliation(s)
- Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Adva Yeheskel
- Bioinformatics Unit, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - David Kornspan
- Department of Bacteriology, Kimron Veterinary Institute, Bet Dagan, Israel
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120
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Carrera M, Böhme K, Gallardo JM, Barros-Velázquez J, Cañas B, Calo-Mata P. Characterization of Foodborne Strains of Staphylococcus aureus by Shotgun Proteomics: Functional Networks, Virulence Factors and Species-Specific Peptide Biomarkers. Front Microbiol 2017; 8:2458. [PMID: 29312172 PMCID: PMC5732212 DOI: 10.3389/fmicb.2017.02458] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/27/2017] [Indexed: 11/13/2022] Open
Abstract
In the present work, we applied a shotgun proteomics approach for the fast and easy characterization of 20 different foodborne strains of Staphylococcus aureus (S. aureus), one of the most recognized foodborne pathogenic bacteria. A total of 644 non-redundant proteins were identified and analyzed via an easy and rapid protein sample preparation procedure. The results allowed the differentiation of several proteome datasets from the different strains (common, accessory, and unique datasets), which were used to determine relevant functional pathways and differentiate the strains into different Euclidean hierarchical clusters. Moreover, a predicted protein-protein interaction network of the foodborne S. aureus strains was created. The whole confidence network contains 77 nodes and 769 interactions. Most of the identified proteins were surface-associated proteins that were related to pathways and networks of energy, lipid metabolism and virulence. Twenty-seven virulence factors were identified, and most of them corresponded to autolysins, N-acetylmuramoyl-L-alanine amidases, phenol-soluble modulins, extracellular fibrinogen-binding proteins and virulence factor EsxA. Potential species-specific peptide biomarkers were screened. Twenty-one species-specific peptide biomarkers, belonging to eight different proteins (nickel-ABC transporter, N-acetylmuramoyl-L-alanine amidase, autolysin, clumping factor A, gram-positive signal peptide YSIRK, cysteine protease/staphopain, transcriptional regulator MarR, and transcriptional regulator Sar-A), were proposed to identify S. aureus. These results constitute the first major dataset of peptides and proteins of foodborne S. aureus strains. This repository may be useful for further studies, for the development of new therapeutic treatments for S. aureus food intoxications and for microbial source-tracking in foodstuffs.
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Affiliation(s)
- Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, Vigo, Spain
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - José M. Gallardo
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, Vigo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
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121
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Errington J, Mickiewicz K, Kawai Y, Wu LJ. L-form bacteria, chronic diseases and the origins of life. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0494. [PMID: 27672147 PMCID: PMC5052740 DOI: 10.1098/rstb.2015.0494] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 12/13/2022] Open
Abstract
The peptidoglycan cell wall is widely conserved across the bacterial domain, suggesting that it appeared early in the evolution of bacteria. It is normally essential but under certain conditions wall-deficient or ‘L-form’ bacteria can be isolated. In Bacillus subtilis this normally requires two genetic changes. The first, exemplified by mutations shutting down wall precursor synthesis, works by increasing membrane synthesis. This promotes the unusual form of proliferation used by L-forms, involving a range of relatively disorganized membrane blebbing or vesiculation events. The secondary class of mutations probably work by relieving oxidative stress that L-forms may incur due to their unbalanced metabolism. Repression or inhibition of cell wall precursor synthesis can stimulate the L-form transition in a wide range of bacteria, of both Gram-positive and -negative lineages. L-forms are completely resistant to most antibiotics working specifically on cell wall synthesis, such as penicillins and cephalosporins, consistent with the many reports of their involvement in various chronic diseases. They are potentially important in biotechnology, because lack of a wall can be advantageous in a range of production or strain improvement applications. Finally, L-forms provide an interesting model system for studying early steps in the evolution of cellular life. This article is part of the themed issue ‘The new bacteriology’.
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Affiliation(s)
- Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE24AX, UK
| | - Katarzyna Mickiewicz
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE24AX, UK
| | - Yoshikazu Kawai
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE24AX, UK
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE24AX, UK
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122
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Lewandowski EM, Lethbridge KG, Sanishvili R, Skiba J, Kowalski K, Chen Y. Mechanisms of proton relay and product release by Class A β-lactamase at ultrahigh resolution. FEBS J 2017; 285:87-100. [PMID: 29095570 DOI: 10.1111/febs.14315] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/15/2017] [Accepted: 10/28/2017] [Indexed: 01/25/2023]
Abstract
The β-lactam antibiotics inhibit penicillin-binding proteins (PBPs) by forming a stable, covalent, acyl-enzyme complex. During the evolution from PBPs to Class A β-lactamases, the β-lactamases acquired Glu166 to activate a catalytic water and cleave the acyl-enzyme bond. Here we present three product complex crystal structures of CTX-M-14 Class A β-lactamase with a ruthenocene-conjugated penicillin-a 0.85 Å resolution structure of E166A mutant complexed with the penilloate product, a 1.30 Å resolution complex structure of the same mutant with the penicilloate product, and a 1.18 Å resolution complex structure of S70G mutant with a penicilloate product epimer-shedding light on the catalytic mechanisms and product inhibition of PBPs and Class A β-lactamases. The E166A-penilloate complex captured the hydrogen bonding network following the protonation of the leaving group and, for the first time, unambiguously show that the ring nitrogen donates a proton to Ser130, which in turn donates a proton to Lys73. These observations indicate that in the absence of Glu166, the equivalent lysine would be neutral in PBPs and therefore capable of serving as the general base to activate the catalytic serine. Together with previous results, this structure suggests a common proton relay network shared by Class A β-lactamases and PBPs, from the catalytic serine to the lysine, and ultimately to the ring nitrogen. Additionally, the E166A-penicilloate complex reveals previously unseen conformational changes of key catalytic residues during the release of the product, and is the first structure to capture the hydrolyzed product in the presence of an unmutated catalytic serine. DATABASE Structural data are available in the PDB database under the accession numbers 5TOP, 5TOY, and 5VLE.
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Affiliation(s)
- Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Kathryn G Lethbridge
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Ruslan Sanishvili
- GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, IL, USA
| | - Joanna Skiba
- Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Poland
| | - Konrad Kowalski
- Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Poland
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
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123
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Zhao H, Patel V, Helmann JD, Dörr T. Don't let sleeping dogmas lie: new views of peptidoglycan synthesis and its regulation. Mol Microbiol 2017; 106:847-860. [PMID: 28975672 DOI: 10.1111/mmi.13853] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/24/2022]
Abstract
Bacterial cell wall synthesis is the target for some of our most powerful antibiotics and has thus been the subject of intense research focus for more than 50 years. Surprisingly, we still lack a fundamental understanding of how bacteria build, maintain and expand their cell wall. Due to technical limitations, directly testing hypotheses about the coordination and biochemistry of cell wall synthesis enzymes or architecture has been challenging, and interpretation of data has therefore often relied on circumstantial evidence and implicit assumptions. A number of recent papers have exploited new technologies, like single molecule tracking and real-time, high resolution temporal mapping of cell wall synthesis processes, to address fundamental questions of bacterial cell wall biogenesis. The results have challenged established dogmas and it is therefore timely to integrate new data and old observations into a new model of cell wall biogenesis in rod-shaped bacteria.
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Affiliation(s)
- Heng Zhao
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Vaidehi Patel
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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124
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Sathiyamoorthy K, Vijayalakshmi J, Tirupati B, Fan L, Saper MA. Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution. J Biol Chem 2017; 292:17626-17642. [PMID: 28887305 DOI: 10.1074/jbc.m117.804997] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 08/13/2017] [Indexed: 11/06/2022] Open
Abstract
In many Gram-negative bacteria, the peptidoglycan synthase PBP1A requires the outer membrane lipoprotein LpoA for constructing a functional peptidoglycan required for bacterial viability. Previously, we have shown that the C-terminal domain of Haemophilus influenzae LpoA (HiLpoA) has a highly conserved, putative substrate-binding cleft between two α/β lobes. Here, we report a 2.0 Å resolution crystal structure of the HiLpoA N-terminal domain. Two subdomains contain tetratricopeptide-like motifs that form a concave groove, but their relative orientation differs by ∼45° from that observed in an NMR structure of the Escherichia coli LpoA N domain. We also determined three 2.0-2.8 Å resolution crystal structures containing four independent full-length HiLpoA molecules. In contrast to an elongated model previously suggested for E. coli LpoA, each HiLpoA formed a U-shaped structure with a different C-domain orientation. This resulted from both N-domain twisting and rotation of the C domain (up to 30°) at the end of the relatively immobile interdomain linker. Moreover, a previously predicted hinge between the lobes of the LpoA C domain exhibited variations of up to 12°. Small-angle X-ray scattering data revealed excellent agreement with a model calculated by normal mode analysis from one of the full-length HiLpoA molecules but even better agreement with an ensemble of this molecule and two of the partially extended normal mode analysis-predicted models. The different LpoA structures helped explain how an outer membrane-anchored LpoA can either withdraw from or extend toward the inner membrane-bound PBP1A through peptidoglycan gaps and hence regulate the synthesis of peptidoglycan necessary for bacterial viability.
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Affiliation(s)
| | | | | | - Lixin Fan
- the Small-Angle X-ray Scattering Core Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702
| | - Mark A Saper
- From the Program in Biophysics and .,the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-5606 and
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125
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Müller A, Klöckner A, Schneider T. Targeting a cell wall biosynthesis hot spot. Nat Prod Rep 2017; 34:909-932. [PMID: 28675405 DOI: 10.1039/c7np00012j] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2017History points to the bacterial cell wall biosynthetic network as a very effective target for antibiotic intervention, and numerous natural product inhibitors have been discovered. In addition to the inhibition of enzymes involved in the multistep synthesis of the macromolecular layer, in particular, interference with membrane-bound substrates and intermediates essential for the biosynthetic reactions has proven a valuable antibacterial strategy. A prominent target within the peptidoglycan biosynthetic pathway is lipid II, which represents a particular "Achilles' heel" for antibiotic attack, as it is readily accessible on the outside of the cytoplasmic membrane. Lipid II is a unique non-protein target that is one of the structurally most conserved molecules in bacterial cells. Notably, lipid II is more than just a target molecule, since sequestration of the cell wall precursor may be combined with additional antibiotic activities, such as the disruption of membrane integrity or disintegration of membrane-bound multi-enzyme machineries. Within the membrane bilayer lipid II is likely organized in specific anionic phospholipid patches that form a particular "landing platform" for antibiotics. Nature has invented a variety of different "lipid II binders" of at least 5 chemical classes, and their antibiotic activities can vary substantially depending on the compounds' physicochemical properties, such as amphiphilicity and charge, and thus trigger diverse cellular effects that are decisive for antibiotic activity.
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Affiliation(s)
- Anna Müller
- Institute of Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
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126
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Qiao Y, Srisuknimit V, Rubino F, Schaefer K, Ruiz N, Walker S, Kahne D. Lipid II overproduction allows direct assay of transpeptidase inhibition by β-lactams. Nat Chem Biol 2017; 13:793-798. [PMID: 28553948 PMCID: PMC5478438 DOI: 10.1038/nchembio.2388] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/13/2017] [Indexed: 01/07/2023]
Abstract
Peptidoglycan is an essential crosslinked polymer that surrounds bacteria and protects them from osmotic lysis. Beta-lactam antibiotics target the final stages of peptidoglycan biosynthesis by inhibiting the transpeptidases that crosslink glycan strands to complete cell wall assembly. Characterization of transpeptidases and their inhibition by beta-lactams has been hampered by lack of access to substrate. We describe a general approach to accumulate Lipid II in bacteria and to obtain large quantities of this cell wall precursor. We demonstrate utility by isolating Staphylococcus aureus Lipid II and reconstituting the synthesis of crosslinked peptidoglycan by the essential penicillin-binding protein 2, PBP2, which catalyzes both glycan polymerization and transpeptidation. We also show that we can compare the potencies of different beta-lactams by directly monitoring transpeptidase inhibition. The methods reported here will enable a better understanding of cell wall biosynthesis and facilitate studies of next-generation transpeptidase inhibitors.
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Affiliation(s)
- Yuan Qiao
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Veerasak Srisuknimit
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Frederick Rubino
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Kaitlin Schaefer
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Natividad Ruiz
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Suzanne Walker
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
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127
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Abstract
Bacillus subtilis is the best described member of the Gram positive bacteria. It is a typical rod shaped bacterium and grows by elongation in its long axis, before dividing at mid cell to generate two similar daughter cells. B. subtilis is a particularly interesting model for cell cycle studies because it also carries out a modified, asymmetrical division during endospore formation, which can be simply induced by starvation. Cell growth occurs strictly by elongation of the rod, which maintains a constant diameter at all growth rates. This process involves expansion of the cell wall, requiring intercalation of new peptidoglycan and teichoic acid material, as well as controlled hydrolysis of existing wall material. Actin-like MreB proteins are the key spatial regulators that orchestrate the plethora of enzymes needed for cell elongation, many of which are thought to assemble into functional complexes called elongasomes. Cell division requires a switch in the orientation of cell wall synthesis and is organised by a tubulin-like protein FtsZ. FtsZ forms a ring-like structure at the site of impending division, which is specified by a range of mainly negative regulators. There it recruits a set of dedicated division proteins to form a structure called the divisome, which brings about the process of division. During sporulation, both the positioning and fine structure of the division septum are altered, and again, several dedicated proteins that contribute specifically to this process have been identified. This chapter summarises our current understanding of elongation and division in B. subtilis, with particular emphasis on the cytoskeletal proteins MreB and FtsZ, and highlights where the major gaps in our understanding remain.
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128
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Cell wall-deficient, L-form bacteria in the 21st century: a personal perspective. Biochem Soc Trans 2017; 45:287-295. [PMID: 28408469 PMCID: PMC5390494 DOI: 10.1042/bst20160435] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 11/19/2022]
Abstract
The peptidoglycan (PG) cell wall is a defining feature of the bacteria. It emerged very early in evolution and must have contributed significantly to the success of these organisms. The wall features prominently in our thinking about bacterial cell function, and its synthesis involves the action of several dozen proteins that are normally essential for viability. Surprisingly, it turns out to be relatively simple to generate bacterial genetic variants called L-forms that completely lack PG. They grow robustly provided that lack of the cell wall is compensated for by an osmoprotective growth medium. Although their existence has been noted and studied on and off for many decades, it is only recently that modern molecular and cellular methods have been applied to L-forms. We used Bacillus subtilis as an experimental model to understand the molecular basis for the L-form switch. Key findings included the discovery that L-forms use an unusual blebbing, or tubulation and scission mechanism to proliferate. This mechanism is completely independent of the normal FtsZ-based division machinery and seems to require only an increased rate of membrane synthesis, leading to an increased surface area-to-volume ratio. Antibiotics that block cell wall precursor synthesis, such as phosphomycin, efficiently induce the L-form switch without the need for genetic change. The same antibiotics turned out to induce a similar L-form switch in a wide range of bacteria, including Escherichia coli, in which we showed that proliferation was again FtsZ-independent. Aside from further basic science, future work on L-forms is likely to focus on their possible role in chronic or recurrent infections, their use as a model in studies of the origins of life, and possibly, biotechnological applications.
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129
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Margulieux KR, Liebov BK, Tirumala VSKKS, Singh A, Bushweller JH, Nakamoto RK, Hughes MA. Bacillus anthracis Peptidoglycan Integrity Is Disrupted by the Chemokine CXCL10 through the FtsE/X Complex. Front Microbiol 2017; 8:740. [PMID: 28496437 PMCID: PMC5406473 DOI: 10.3389/fmicb.2017.00740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/10/2017] [Indexed: 01/07/2023] Open
Abstract
The antimicrobial activity of the chemokine CXCL10 against vegetative cells of Bacillus anthracis occurs via both bacterial FtsE/X-dependent and-independent pathways. Previous studies established that the FtsE/X-dependent pathway was mediated through interaction of the N-terminal region(s) of CXCL10 with a functional FtsE/X complex, while the FtsE/X-independent pathway was mediated through the C-terminal α-helix of CXCL10. Both pathways result in cell lysis and death of B. anthracis. In other bacterial species, it has been shown that FtsE/X is involved in cellular elongation though activation of complex-associated peptidoglycan hydrolases. Thus, we hypothesized that the CXCL10-mediated killing of vegetative cells of B. anthracis through the FtsE/X-dependent pathway resulted from the disruption of peptidoglycan processing. Immunofluorescence microscopy studies using fluorescent peptidoglycan probes revealed that incubation of B. anthracis Sterne (parent) strain with CXCL10 or a C-terminal truncated CXCL10 (CTTC) affected peptidoglycan processing and/or incorporation of precursors into the cell wall. B. anthracis ΔftsX or ftsE(K123A/D481N) mutant strains, which lacked a functional FtsE/X complex, exhibited little to no evidence of disruption in peptidoglycan processing by either CXCL10 or CTTC. Additional studies demonstrated that the B. anthracis parent strain exhibited a statistically significant increase in peptidoglycan release in the presence of either CXCL10 or CTTC. While B. anthracis ΔftsX strain showed increased peptidoglycan release in the presence of CXCL10, no increase was observed with CTTC, suggesting that the FtsE/X-independent pathway was responsible for the activity observed with CXCL10. These results indicate that FtsE/X-dependent killing of vegetative cells of B. anthracis results from a loss of cell wall integrity due to disruption of peptidoglycan processing and suggest that FtsE/X may be an important antimicrobial target to study in the search for alternative microbial therapeutics.
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Affiliation(s)
- Katie R Margulieux
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, University of Virginia, CharlottesvilleVA, USA
| | - Benjamin K Liebov
- Department of Chemistry, University of Virginia, CharlottesvilleVA, USA
| | - Venkata S K K S Tirumala
- Department of Molecular Physiology and Biological Physics, University of Virginia, CharlottesvilleVA, USA
| | - Arpita Singh
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, University of Virginia, CharlottesvilleVA, USA
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, CharlottesvilleVA, USA
| | - Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, CharlottesvilleVA, USA
| | - Molly A Hughes
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, University of Virginia, CharlottesvilleVA, USA
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130
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Progress and prospects for small-molecule probes of bacterial imaging. Nat Chem Biol 2017; 12:472-8. [PMID: 27315537 DOI: 10.1038/nchembio.2109] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 05/13/2016] [Indexed: 11/09/2022]
Abstract
Fluorescence microscopy is an essential tool for the exploration of cell growth, division, transcription and translation in eukaryotes and prokaryotes alike. Despite the rapid development of techniques to study bacteria, the size of these organisms (1-10 μm) and their robust and largely impenetrable cell envelope present major challenges in imaging experiments. Fusion-based strategies, such as attachment of the protein of interest to a fluorescent protein or epitope tag, are by far the most common means for examining protein localization and expression in prokaryotes. While valuable, the use of genetically encoded tags can result in mislocalization or altered activity of the desired protein, does not provide a readout of the catalytic state of enzymes and cannot enable visualization of many other important cellular components, such as peptidoglycan, lipids, nucleic acids or glycans. Here, we highlight the use of biomolecule-specific small-molecule probes for imaging in bacteria.
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131
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 550] [Impact Index Per Article: 78.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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132
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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133
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Lohani M, Dhasmana A, Haque S, Wahid M, Jawed A, Dar SA, Mandal RK, Areeshi MY, Khan S. Proteome mining for the identification and in-silico characterization of putative drug targets of multi-drug resistant Clostridium difficile strain 630. J Microbiol Methods 2017; 136:6-10. [PMID: 28235560 DOI: 10.1016/j.mimet.2017.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/19/2017] [Accepted: 02/19/2017] [Indexed: 10/20/2022]
Abstract
Clostridium difficile is an enteric pathogen that causes approximately 20% to 30% of antibiotic-associated diarrhea. In recent years, there has been a substantial rise in the rate of C. difficile infections as well as the emergence of virulent and antibiotic resistant C. difficile strains. So, there is an urgent need for the identification of therapeutic potential targets and development of new drugs for the treatment and prevention of C. difficile infections. In the current study, we used a hybrid approach by combining sequence similarity-based approach and protein-protein interaction network topology-based approach to identify and characterize the potential drug targets of C. difficile. A total of 155 putative drug targets of C. difficile were identified and the metabolic pathway analysis of these putative drug targets using DAVID revealed that 46 of them are involved in 9 metabolic pathways. In-silico characterization of these proteins identified seven proteins involved in pathogen-specific peptidoglycan biosynthesis pathway. Three promising targets viz. homoserine dehydrogenase, aspartate-semialdehyde dehydrogenase and aspartokinase etc. were found to be involved in multiple enzymatic pathways of the pathogen. These 3 drug targets are of particular interest as they can be used for developing effective drugs against multi-drug resistant C. difficile strain 630 in the near future.
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Affiliation(s)
- Mohtashim Lohani
- Department of Biosciences, Integral University, Lucknow, India; Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia.
| | - Anupam Dhasmana
- Department of Biotechnology, Amity University, Lucknow, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sajad A Dar
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saif Khan
- College of Applied Medical Sciences, Hail University, Hail, Saudi Arabia
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134
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Xin Q, Liu Q, Geng L, Fang Q, Gong JR. Chiral Nanoparticle as a New Efficient Antimicrobial Nanoagent. Adv Healthc Mater 2017; 6. [PMID: 28026134 DOI: 10.1002/adhm.201601011] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/29/2016] [Indexed: 11/10/2022]
Abstract
d-type functionalized nanoparticles (NPs) can bind to MurD ligase with high affinity and inhibit its peptidoglycan synthetic enzyme activity, and finally cause bacterial killing. In contrast, its L-type counterpart displays a negligible effect, indicating that the chiral structure of the functionalized NPs plays an essential role in their binding interaction with MurD and therefore the antibacterial activity.
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Affiliation(s)
- Qi Xin
- CAS Center of Excellence for Nanoscience; CAS Key Laboratory for Nanosystem and Hierarchical Fabrication; National Center for Nanoscience and Technology; 11 Beiyitiao Zhongguancun Beijing 100190 P. R. China
| | - Qian Liu
- CAS Center of Excellence for Nanoscience; CAS Key Laboratory for Nanosystem and Hierarchical Fabrication; National Center for Nanoscience and Technology; 11 Beiyitiao Zhongguancun Beijing 100190 P. R. China
| | - Lingling Geng
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety; National Center for Nanoscience and Technology; 11 Beiyitiao Zhongguancun Beijing 100190 P. R. China
| | - Qiaojun Fang
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety; National Center for Nanoscience and Technology; 11 Beiyitiao Zhongguancun Beijing 100190 P. R. China
| | - Jian Ru Gong
- CAS Center of Excellence for Nanoscience; CAS Key Laboratory for Nanosystem and Hierarchical Fabrication; National Center for Nanoscience and Technology; 11 Beiyitiao Zhongguancun Beijing 100190 P. R. China
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135
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Single polysaccharide assembly protein that integrates polymerization, termination, and chain-length quality control. Proc Natl Acad Sci U S A 2017; 114:E1215-E1223. [PMID: 28137848 DOI: 10.1073/pnas.1613609114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Lipopolysaccharides (LPS) are essential outer membrane glycolipids in most gram-negative bacteria. Biosynthesis of the O-antigenic polysaccharide (OPS) component of LPS follows one of three widely distributed strategies, and similar processes are used to assemble other bacterial surface glycoconjugates. This study focuses on the ATP-binding cassette (ABC) transporter-dependent pathway, where glycans are completed on undecaprenyl diphosphate carriers at the cytosol:membrane interface, before export by the ABC transporter. We describe Raoultella terrigena WbbB, a prototype for a family of proteins that, remarkably, integrates several key activities in polysaccharide biosynthesis into a single polypeptide. WbbB contains three glycosyltransferase (GT) modules. Each of the GT102 and GT103 modules characterized here represents a previously unrecognized GT family. They form a polymerase, generating a polysaccharide of [4)-α-Rhap-(1→3)-β-GlcpNAc-(1→] repeat units. The polymer chain is terminated by a β-linked Kdo (3-deoxy-d-manno-oct-2-ulosonic acid) residue added by a third GT module belonging to the recently discovered GT99 family. The polymerase GT modules are separated from the GT99 chain terminator by a coiled-coil structure that forms a molecular ruler to determine product length. Different GT modules in the polymerase domains of other family members produce diversified OPS structures. These findings offer insight into glycan assembly mechanisms and the generation of antigenic diversity as well as potential tools for glycoengineering.
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136
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Mahasenan KV, Molina R, Bouley R, Batuecas MT, Fisher JF, Hermoso JA, Chang M, Mobashery S. Conformational Dynamics in Penicillin-Binding Protein 2a of Methicillin-Resistant Staphylococcus aureus, Allosteric Communication Network and Enablement of Catalysis. J Am Chem Soc 2017; 139:2102-2110. [PMID: 28099001 DOI: 10.1021/jacs.6b12565] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of the β-lactam antibacterials is the functionally irreversible acylation of the enzymes that catalyze the cross-linking steps in the biosynthesis of their peptidoglycan cell wall. The Gram-positive pathogen Staphylococcus aureus uses one primary resistance mechanism. An enzyme, called penicillin-binding protein 2a (PBP2a), is brought into this biosynthetic pathway to complete the cross-linking. PBP2a effectively discriminates against the β-lactam antibiotics as potential inhibitors, and in favor of the peptidoglycan substrate. The basis for this discrimination is an allosteric site, distal from the active site, that when properly occupied concomitantly opens the gatekeeper residues within the active site and realigns the conformation of key residues to permit catalysis. We address the molecular basis of this regulation using crystallographic studies augmented by computational analyses. The crystal structures of three β-lactams (oxacillin, cefepime, ceftazidime) complexes with PBP2a-each with the β-lactam in the allosteric site-defined (with preceding PBP2a structures) as the "open" or "partially open" PBP2a states. A particular loop motion adjacent to the active site is identified as the driving force for the active-site conformational change that accompanies active-site opening. Correlation of this loop motion to effector binding at the allosteric site, in order to identify the signaling pathway, was accomplished computationally in reference to the known "closed" apo-PBP2a X-ray crystal structure state. This correlation enabled the computational simulation of the structures coinciding with initial peptidoglycan substrate binding to PBP2a, acyl enzyme formation, and acyl transfer to a second peptidoglycan substrate to attain cross-linking. These studies offer important insights into the structural bases for allosteric site-to-active site communication and for β-lactam mimicry of the peptidoglycan substrates, as foundational to the mechanistic understanding of emerging PBP2a resistance mutations.
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Affiliation(s)
- Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid, Spain
| | - Renee Bouley
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - María T Batuecas
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid, Spain
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid, Spain
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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137
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Emami K, Guyet A, Kawai Y, Devi J, Wu LJ, Allenby N, Daniel RA, Errington J. RodA as the missing glycosyltransferase in Bacillus subtilis and antibiotic discovery for the peptidoglycan polymerase pathway. Nat Microbiol 2017; 2:16253. [PMID: 28085152 PMCID: PMC5568705 DOI: 10.1038/nmicrobiol.2016.253] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/15/2016] [Indexed: 11/08/2022]
Abstract
The bacterial cell wall is a highly conserved essential component of most bacterial groups. It is the target for our most frequently used antibiotics and provides important small molecules that trigger powerful innate immune responses. The wall is composed of glycan strands crosslinked by short peptides. For many years, the penicillin-binding proteins were thought to be the key enzymes required for wall synthesis. RodA and possibly other proteins in the wider SEDS (shape, elongation, division and sporulation) family have now emerged as a previously unknown class of essential glycosyltranferase enzymes, which play key morphogenetic roles in bacterial cell wall synthesis. We provide evidence in support of this role and the discovery of small natural product molecules that probably target these enzymes. The SEDS proteins have exceptional potential as targets for new antibacterial therapeutic agents.
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Affiliation(s)
- Kaveh Emami
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Aurelie Guyet
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Yoshikazu Kawai
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Jenny Devi
- Demuris Ltd, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Ling J Wu
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Nick Allenby
- Demuris Ltd, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Richard A Daniel
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Jeff Errington
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
- Demuris Ltd, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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138
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Antibacterial New Target Discovery: Sentinel Examples, Strategies, and Surveying Success. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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139
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Wei Y, Qiu W, Zhou XD, Zheng X, Zhang KK, Wang SD, Li YQ, Cheng L, Li JY, Xu X, Li MY. Alanine racemase is essential for the growth and interspecies competitiveness of Streptococcus mutans. Int J Oral Sci 2016; 8:231-238. [PMID: 27740612 PMCID: PMC5168415 DOI: 10.1038/ijos.2016.34] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 02/05/2023] Open
Abstract
D-alanine (D-Ala) is an essential amino acid that has a key role in bacterial cell wall synthesis. Alanine racemase (Alr) is a unique enzyme that interconverts L-alanine and D-alanine in most bacteria, making this enzyme a potential target for antimicrobial drug development. Streptococcus mutans is a major causative factor of dental caries. The factors involved in the survival, virulence and interspecies interactions of S. mutans could be exploited as potential targets for caries control. The current study aimed to investigate the physiological role of Alr in S. mutans. We constructed alr mutant strain of S. mutans and evaluated its phenotypic traits and interspecies competitiveness compared with the wild-type strain. We found that alr deletion was lethal to S. mutans. A minimal supplement of D-Ala (150 μg·mL-1) was required for the optimal growth of the alr mutant. The depletion of D-alanine in the growth medium resulted in cell wall perforation and cell lysis in the alr mutant strain. We also determined the compromised competitiveness of the alr mutant strain relative to the wild-type S. mutans against other oral streptococci (S. sanguinis or S. gordonii), demonstrated using either conditioned medium assays or dual-species fluorescent in situ hybridization analysis. Given the importance and necessity of alr to the growth and competitiveness of S. mutans, Alr may represent a promising target to modulate the cariogenicity of oral biofilms and to benefit the management of dental caries.
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Affiliation(s)
- Yuan Wei
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wei Qiu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xue-Dong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Zheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ke-Ke Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shi-Da Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yu-Qing Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ji-Yao Li
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ming-Yun Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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140
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CozE is a member of the MreCD complex that directs cell elongation in Streptococcus pneumoniae. Nat Microbiol 2016; 2:16237. [PMID: 27941863 DOI: 10.1038/nmicrobiol.2016.237] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 10/19/2016] [Indexed: 11/08/2022]
Abstract
Most bacterial cells are surrounded by a peptidoglycan cell wall that is essential for their integrity. The major synthases of this exoskeleton are called penicillin-binding proteins (PBPs)1,2. Surprisingly little is known about how cells control these enzymes, given their importance as drug targets. In the model Gram-negative bacterium Escherichia coli, outer membrane lipoproteins are critical activators of the class A PBPs (aPBPs)3,4, bifunctional synthases capable of polymerizing and crosslinking peptidoglycan to build the exoskeletal matrix1. Regulators of PBP activity in Gram-positive bacteria have yet to be discovered but are likely to be distinct due to the absence of an outer membrane. To uncover Gram-positive PBP regulatory factors, we used transposon-sequencing (Tn-Seq)5 to screen for mutations affecting the growth of Streptococcus pneumoniae cells when the aPBP synthase PBP1a was inactivated. Our analysis revealed a set of genes that were essential for growth in wild-type cells yet dispensable when pbp1a was deleted. The proteins encoded by these genes include the conserved cell wall elongation factors MreC and MreD2,6,7, as well as a membrane protein of unknown function (SPD_0768) that we have named CozE (coordinator of zonal elongation). Our results indicate that CozE is a member of the MreCD complex of S. pneumoniae that directs the activity of PBP1a to the midcell plane where it promotes zonal cell elongation and normal morphology. CozE homologues are broadly distributed among bacteria, suggesting that they represent a widespread family of morphogenic proteins controlling cell wall biogenesis by the PBPs.
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141
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van't Veer IL, Leloup NOL, Egan AJF, Janssen BJC, Martin NI, Vollmer W, Breukink E. Site-Specific Immobilization of the Peptidoglycan Synthase PBP1B on a Surface Plasmon Resonance Chip Surface. Chembiochem 2016; 17:2250-2256. [PMID: 27709766 PMCID: PMC5298014 DOI: 10.1002/cbic.201600461] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 12/23/2022]
Abstract
Surface plasmon resonance (SPR) is one of the most powerful label-free methods to determine the kinetic parameters of molecular interactions in real time and in a highly sensitive way. Penicillin-binding proteins (PBPs) are peptidoglycan synthesis enzymes present in most bacteria. Established protocols to analyze interactions of PBPs by SPR involve immobilization to an ampicillin-coated chip surface (a β-lactam antibiotic mimicking its substrate), thereby forming a covalent complex with the PBPs transpeptidase (TP) active site. However, PBP interactions measured with a substrate-bound TP domain potentially affect interactions near the TPase active site. Furthermore, in vivo PBPs are anchored in the inner membrane by an N-terminal transmembrane helix, and hence immobilization at the C-terminal TPase domain gives an orientation contrary to the in vivo situation. We designed a new procedure: immobilization of PBP by copper-free click chemistry at an azide incorporated in the N terminus. In a proof-of-principle study, we immobilized Escherichia coli PBP1B on an SPR chip surface and used this for the analysis of the well-characterized interaction of PBP1B with LpoB. The site-specific incorporation of the azide affords control over protein orientation, thereby resulting in a homogeneous immobilization on the chip surface. This method can be used to study topology-dependent interactions of any (membrane) protein.
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Affiliation(s)
- Inge L. van't Veer
- Department of Membrane Biochemistry and BiophysicsUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Nadia O. L. Leloup
- Crystal and Structural ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Alexander J. F. Egan
- The Centre for Bacterial Cell BiologyNewcastle UniversityRichardson RoadNE2 4AX, Newcastle upon TyneUK
| | - Bert J. C. Janssen
- Crystal and Structural ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 993584 CGUtrechtThe Netherlands
| | - Waldemar Vollmer
- The Centre for Bacterial Cell BiologyNewcastle UniversityRichardson RoadNE2 4AX, Newcastle upon TyneUK
| | - Eefjan Breukink
- Department of Membrane Biochemistry and BiophysicsUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
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142
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Biochemical and Structural Analysis of a Novel Esterase from Caulobacter crescentus related to Penicillin-Binding Protein (PBP). Sci Rep 2016; 6:37978. [PMID: 27905486 PMCID: PMC5131357 DOI: 10.1038/srep37978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/03/2016] [Indexed: 01/16/2023] Open
Abstract
Considering that the prevalence of antibiotic-resistant pathogenic bacteria is largely increasing, a thorough understanding of penicillin-binding proteins (PBPs) is of great importance and crucial significance because this enzyme family is a main target of β-lactam-based antibiotics. In this work, combining biochemical and structural analysis, we present new findings that provide novel insights into PBPs. Here, a novel PBP homologue (CcEstA) from Caulobacter crescentus CB15 was characterized using native-PAGE, mass spectrometry, gel filtration, CD spectroscopy, fluorescence, reaction kinetics, and enzyme assays toward various substrates including nitrocefin. Furthermore, the crystal structure of CcEstA was determined at a 1.9 Å resolution. Structural analyses showed that CcEstA has two domains: a large α/β domain and a small α-helix domain. A nucleophilic serine (Ser68) residue is located in a hydrophobic groove between the two domains along with other catalytic residues (Lys71 and Try157). Two large flexible loops (UL and LL) of CcEstA are proposed to be involved in the binding of incoming substrates. In conclusion, CcEstA could be described as a paralog of the group that contains PBPs and β-lactamases. Therefore, this study could provide new structural and functional insights into the understanding this protein family.
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143
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Christel S, Fridlund J, Watkin EL, Dopson M. Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile. Extremophiles 2016; 20:903-913. [PMID: 27783177 PMCID: PMC5085989 DOI: 10.1007/s00792-016-0882-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 10/10/2016] [Indexed: 11/17/2022]
Abstract
Acidithiobacillus ferrivorans is an acidophilic bacterium that represents a substantial proportion of the microbial community in a low temperature mining waste stream. Due to its ability to grow at temperatures below 15 °C, it has previously been classified as 'psychrotolerant'. Low temperature-adapted microorganisms have strategies to grow at cold temperatures such as the production of cold acclimation proteins, DEAD/DEAH box helicases, and compatible solutes plus increasing their cellular membrane fluidity. However, little is known about At. ferrivorans adaptation strategies employed during culture at its temperature extremes. In this study, we report the transcriptomic response of At. ferrivorans SS3 to culture at 8 °C compared to 20 °C. Analysis revealed 373 differentially expressed genes of which, the majority were of unknown function. Only few changes in transcript counts of genes previously described to be cold adaptation genes were detected. Instead, cells cultured at cold (8 °C) altered the expression of a wide range of genes ascribed to functions in transcription, translation, and energy production. It is, therefore, suggested that a temperature of 8 °C imposed little cold stress on At. ferrivorans, underlining its adaptation to growth in the cold as well as suggesting it should be classified as a 'eurypsychrophile'.
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Affiliation(s)
- Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Jimmy Fridlund
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Elizabeth L Watkin
- School of Biomedical Sciences, Curtin University, Perth, 6845, Australia
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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144
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Glycolipid substrates for ABC transporters required for the assembly of bacterial cell-envelope and cell-surface glycoconjugates. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1394-1403. [PMID: 27793707 DOI: 10.1016/j.bbalip.2016.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 01/07/2023]
Abstract
Glycoconjugates, molecules that contain sugar components, are major components of the cell envelopes of bacteria and cover much of their exposed surfaces. These molecules are involved in interactions with the surrounding environment and, in pathogens, play critical roles in the interplay with the host immune system. Despite the remarkable diversity in glycoconjugate structures, most are assembled by glycosyltransferases that act on lipid acceptors at the cytosolic membrane. The resulting glycolipids are then transported to the cell surface in processes that frequently begin with ATP-binding cassette transporters. This review summarizes current understanding of the structure and biosynthesis of glycolipid substrates and the structure and functions of their transporters. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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145
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Tan XE, Neoh HM, Looi ML, Chin SF, Cui L, Hiramatsu K, Hussin S, Jamal R. Activated ADI pathway: the initiator of intermediate vancomycin resistance in Staphylococcus aureus. Can J Microbiol 2016; 63:260-264. [PMID: 28059579 DOI: 10.1139/cjm-2016-0439] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Comparative proteomic profiling between 2 vancomycin-intermediate Staphylococcus aureus (VISA) strains, Mu50Ω-vraSm and Mu50Ω-vraSm-graRm, and vancomycin-susceptible S. aureus (VSSA) strain Mu50Ω revealed upregulated levels of catabolic ornithine carbamoyltransferase (ArcB) of the arginine catabolism pathway in VISA strains. Subsequent analyses showed that the VISA strains have higher levels of cellular ATP and ammonia, which are by-products of arginine catabolism, and displayed thicker cell walls. We postulate that elevated cytoplasmic ammonia and ATP molecules, resulting from activated arginine catabolism upon acquisition of vraS and graR mutations, are important requirements facilitating cell wall biosynthesis, thereby contributing to thickened cell wall and consequently reduced vancomycin susceptibility in VISA strains.
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Affiliation(s)
- Xin-Ee Tan
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Hui-Min Neoh
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.,b Department of Bacteriology, School of Medicine, Juntendo University, Japan
| | - Mee-Lee Looi
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.,c Taylor's University Lakeside Campus, School of Biosciences, Malaysia
| | - Siok Fong Chin
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Longzhu Cui
- d Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Japan
| | - Keiichi Hiramatsu
- b Department of Bacteriology, School of Medicine, Juntendo University, Japan
| | - Salasawati Hussin
- e Department of Medical Microbiology and Immunology, Universiti Kebangsaan Malaysia, Malaysia
| | - Rahman Jamal
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
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146
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Depletion of Undecaprenyl Pyrophosphate Phosphatases Disrupts Cell Envelope Biogenesis in Bacillus subtilis. J Bacteriol 2016; 198:2925-2935. [PMID: 27528508 DOI: 10.1128/jb.00507-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/02/2016] [Indexed: 11/20/2022] Open
Abstract
The integrity of the bacterial cell envelope is essential to sustain life by countering the high turgor pressure of the cell and providing a barrier against chemical insults. In Bacillus subtilis, synthesis of both peptidoglycan and wall teichoic acids requires a common C55 lipid carrier, undecaprenyl-pyrophosphate (UPP), to ferry precursors across the cytoplasmic membrane. The synthesis and recycling of UPP requires a phosphatase to generate the monophosphate form Und-P, which is the substrate for peptidoglycan and wall teichoic acid synthases. Using an optimized clustered regularly interspaced short palindromic repeat (CRISPR) system with catalytically inactive ("dead") CRISPR-associated protein 9 (dCas9)-based transcriptional repression system (CRISPR interference [CRISPRi]), we demonstrate that B. subtilis requires either of two UPP phosphatases, UppP or BcrC, for viability. We show that a third predicted lipid phosphatase (YodM), with homology to diacylglycerol pyrophosphatases, can also support growth when overexpressed. Depletion of UPP phosphatase activity leads to morphological defects consistent with a failure of cell envelope synthesis and strongly activates the σM-dependent cell envelope stress response, including bcrC, which encodes one of the two UPP phosphatases. These results highlight the utility of an optimized CRISPRi system for the investigation of synthetic lethal gene pairs, clarify the nature of the B. subtilis UPP-Pase enzymes, and provide further evidence linking the σM regulon to cell envelope homeostasis pathways. IMPORTANCE The emergence of antibiotic resistance among bacterial pathogens is of critical concern and motivates efforts to develop new therapeutics and increase the utility of those already in use. The lipid II cycle is one of the most frequently targeted processes for antibiotics and has been intensively studied. Despite these efforts, some steps have remained poorly defined, partly due to genetic redundancy. CRISPRi provides a powerful tool to investigate the functions of essential genes and sets of genes. Here, we used an optimized CRISPRi system to demonstrate functional redundancy of two UPP phosphatases that are required for the conversion of the initially synthesized UPP lipid carrier to Und-P, the substrate for the synthesis of the initial lipid-linked precursors in peptidoglycan and wall teichoic acid synthesis.
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147
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Domínguez-Gil T, Lee M, Acebrón-Avalos I, Mahasenan KV, Hesek D, Dik DA, Byun B, Lastochkin E, Fisher JF, Mobashery S, Hermoso JA. Activation by Allostery in Cell-Wall Remodeling by a Modular Membrane-Bound Lytic Transglycosylase from Pseudomonas aeruginosa. Structure 2016; 24:1729-1741. [PMID: 27618662 DOI: 10.1016/j.str.2016.07.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 11/19/2022]
Abstract
Bacteria grow and divide without loss of cellular integrity. This accomplishment is notable, as a key component of their cell envelope is a surrounding glycopeptide polymer. In Gram-negative bacteria this polymer-the peptidoglycan-grows by the difference between concurrent synthesis and degradation. The regulation of the enzymatic ensemble for these activities is poorly understood. We report herein the structural basis for the control of one such enzyme, the lytic transglycosylase MltF of Pseudomonas aeruginosa. Its structure comprises two modules: an ABC-transporter-like regulatory module and a catalytic module. Occupancy of the regulatory module by peptidoglycan-derived muropeptides effects a dramatic and long-distance (40 Å) conformational change, occurring over the entire protein structure, to open its active site for catalysis. This discovery of the molecular basis for the allosteric control of MltF catalysis is foundational to further study of MltF within the complex enzymatic orchestration of the dynamic peptidoglycan.
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Affiliation(s)
- Teresa Domínguez-Gil
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Iván Acebrón-Avalos
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - David A Dik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Byungjin Byun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Juan A Hermoso
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
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148
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The Membrane Steps of Bacterial Cell Wall Synthesis as Antibiotic Targets. Antibiotics (Basel) 2016; 5:antibiotics5030028. [PMID: 27571111 PMCID: PMC5039524 DOI: 10.3390/antibiotics5030028] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 11/23/2022] Open
Abstract
Peptidoglycan is the major component of the cell envelope of virtually all bacteria. It has structural roles and acts as a selective sieve for molecules from the outer environment. Peptidoglycan synthesis is therefore one of the most important biogenesis pathways in bacteria and has been studied extensively over the last twenty years. The pathway starts in the cytoplasm, continues in the cytoplasmic membrane and finishes in the periplasmic space, where the precursor is polymerized into the peptidoglycan layer. A number of proteins involved in this pathway, such as the Mur enzymes and the penicillin binding proteins (PBPs), have been studied and regarded as good targets for antibiotics. The present review focuses on the membrane steps of peptidoglycan synthesis that involve two enzymes, MraY and MurG, the inhibitors of these enzymes and the inhibition mechanisms. We also discuss the challenges of targeting these two cytoplasmic membrane (associated) proteins in bacterial cells and the perspectives on how to overcome the issues.
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149
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Vivoli M, Isupov MN, Nicholas R, Hill A, Scott AE, Kosma P, Prior JL, Harmer NJ. Unraveling the B. pseudomallei Heptokinase WcbL: From Structure to Drug Discovery. ACTA ACUST UNITED AC 2016; 22:1622-32. [PMID: 26687481 PMCID: PMC4691232 DOI: 10.1016/j.chembiol.2015.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/20/2015] [Accepted: 10/31/2015] [Indexed: 11/25/2022]
Abstract
Gram-negative bacteria utilize heptoses as part of their repertoire of extracellular polysaccharide virulence determinants. Disruption of heptose biosynthesis offers an attractive target for novel antimicrobials. A critical step in the synthesis of heptoses is their 1-O phosphorylation, mediated by kinases such as HldE or WcbL. Here, we present the structure of WcbL from Burkholderia pseudomallei. We report that WcbL operates through a sequential ordered Bi-Bi mechanism, loading the heptose first and then ATP. We show that dimeric WcbL binds ATP anti-cooperatively in the absence of heptose, and cooperatively in its presence. Modeling of WcbL suggests that heptose binding causes an elegant switch in the hydrogen-bonding network, facilitating the binding of a second ATP molecule. Finally, we screened a library of drug-like fragments, identifying hits that potently inhibit WcbL. Our results provide a novel mechanism for control of substrate binding and emphasize WcbL as an attractive anti-microbial target for Gram-negative bacteria.
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Affiliation(s)
- Mirella Vivoli
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Michail N Isupov
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rebecca Nicholas
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew Hill
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew E Scott
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Paul Kosma
- University of Natural Resources and Life Sciences-Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Joann L Prior
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Nicholas J Harmer
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK.
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150
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Gupta SK, Gross R, Dandekar T. An antibiotic target ranking and prioritization pipeline combining sequence, structure and network-based approaches exemplified for Serratia marcescens. Gene 2016; 591:268-278. [PMID: 27425866 DOI: 10.1016/j.gene.2016.07.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/26/2016] [Accepted: 07/12/2016] [Indexed: 01/20/2023]
Abstract
We investigate a drug target screening pipeline comparing sequence, structure and network-based criteria for prioritization. Serratia marcescens, an opportunistic pathogen, serves as test case. We rank according to (i) availability of three dimensional structures and lead compounds, (ii) not occurring in man and general sequence conservation information, and (iii) network information on the importance of the protein (conserved protein-protein interactions; metabolism; reported to be an essential gene in other organisms). We identify 45 potential anti-microbial drug targets in S. marcescens with KdsA involved in LPS biosynthesis as top candidate drug target. LpxC and FlgB are further top-ranked targets identified by interactome analysis not suggested before for S. marcescens. Pipeline, targets and complementarity of the three approaches are evaluated by available experimental data and genetic evidence and against other antibiotic screening pipelines. This supports reliable drug target identification and prioritization for infectious agents (bacteria, parasites, fungi) by these bundled complementary criteria.
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Affiliation(s)
- Shishir K Gupta
- Department of Bioinformatics, Biocenter, Am Hubland, D-97074 Würzburg, Germany; Department of Microbiology, Biocenter, Am Hubland, D-97074 Würzburg, Germany.
| | - Roy Gross
- Department of Microbiology, Biocenter, Am Hubland, D-97074 Würzburg, Germany.
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, D-97074 Würzburg, Germany; EMBL Heidelberg, BioComputing Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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