1
|
Hogan AM, Motnenko A, Rahman ASMZ, Cardona ST. Cell envelope structural and functional contributions to antibiotic resistance in Burkholderia cenocepacia. J Bacteriol 2024; 206:e0044123. [PMID: 38501654 PMCID: PMC11025338 DOI: 10.1128/jb.00441-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Antibiotic activity is limited by the physical construction of the Gram-negative cell envelope. Species of the Burkholderia cepacia complex (Bcc) are known as intrinsically multidrug-resistant opportunistic pathogens with low permeability cell envelopes. Here, we re-examined a previously performed chemical-genetic screen of barcoded transposon mutants in B. cenocepacia K56-2, focusing on cell envelope structural and functional processes. We identified structures mechanistically important for resistance to singular and multiple antibiotic classes. For example, susceptibility to novobiocin, avibactam, and the LpxC inhibitor, PF-04753299, was linked to the BpeAB-OprB efflux pump, suggesting these drugs are substrates for this pump in B. cenocepacia. Defects in peptidoglycan precursor synthesis specifically increased susceptibility to cycloserine and revealed a new putative amino acid racemase, while defects in divisome accessory proteins increased susceptibility to multiple β-lactams. Additionally, disruption of the periplasmic disulfide bond formation system caused pleiotropic defects on outer membrane integrity and β-lactamase activity. Our findings highlight the layering of resistance mechanisms in the structure and function of the cell envelope. Consequently, we point out processes that can be targeted for developing antibiotic potentiators.IMPORTANCEThe Gram-negative cell envelope is a double-layered physical barrier that protects cells from extracellular stressors, such as antibiotics. The Burkholderia cell envelope is known to contain additional modifications that reduce permeability. We investigated Burkholderia cell envelope factors contributing to antibiotic resistance from a genome-wide view by re-examining data from a transposon mutant library exposed to an antibiotic panel. We identified susceptible phenotypes for defects in structures and functions in the outer membrane, periplasm, and cytoplasm. Overall, we show that resistance linked to the cell envelope is multifaceted and provides new targets for the development of antibiotic potentiators.
Collapse
Affiliation(s)
- Andrew M. Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Silvia T. Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
2
|
Kuroda K, Nakajima M, Nakai R, Hirakata Y, Kagemasa S, Kubota K, Noguchi TQP, Yamamoto K, Satoh H, Nobu MK, Narihiro T. Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems. mBio 2024; 15:e0310223. [PMID: 38323857 PMCID: PMC10936435 DOI: 10.1128/mbio.03102-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
To verify whether members of the phylum Candidatus Patescibacteria parasitize archaea, we applied cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses on the Patescibacteria-enriched cultures derived from a methanogenic bioreactor. Amendment of cultures with exogenous methanogenic archaea, acetate, amino acids, and nucleoside monophosphates increased the relative abundance of Ca. Patescibacteria. The predominant Ca. Patescibacteria were families Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae, and the former showed positive linear relationships (r2 ≥ 0.70) Methanothrix in their relative abundances, suggesting related growth patterns. Methanothrix and Methanospirillum cells with attached Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae, respectively, had significantly lower cellular activity than those of the methanogens without Ca. Patescibacteria, as extrapolated from fluorescence in situ hybridization-based fluorescence. We also observed that parasitized methanogens often had cell surface deformations. Some Methanothrix-like filamentous cells were dented where the submicron cells were attached. Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae highly expressed extracellular enzymes, and based on structural predictions, some contained peptidoglycan-binding domains with potential involvement in host cell attachment. Collectively, we propose that the interactions of Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae with methanogenic archaea are parasitisms.IMPORTANCECulture-independent DNA sequencing approaches have explored diverse yet-to-be-cultured microorganisms and have significantly expanded the tree of life in recent years. One major lineage of the domain Bacteria, Ca. Patescibacteria (also known as candidate phyla radiation), is widely distributed in natural and engineered ecosystems and has been thought to be dependent on host bacteria due to the lack of several biosynthetic pathways and small cell/genome size. Although bacteria-parasitizing or bacteria-preying Ca. Patescibacteria have been described, our recent studies revealed that some lineages can specifically interact with archaea. In this study, we provide strong evidence that the relationship is parasitic, shedding light on overlooked roles of Ca. Patescibacteria in anaerobic habitats.
Collapse
Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Meri Nakajima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Hokkaido, Japan
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Yuga Hirakata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Shuka Kagemasa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
- Department of Civil and Environmental Engineering, National Institute of Technology, Anan College, Anan, Tokushima, Japan
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan
| | - Taro Q. P. Noguchi
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, Miyakonojo, Miyazaki, Japan
| | - Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Hokkaido, Japan
| | - Masaru K. Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| |
Collapse
|
3
|
Williams AH, Wheeler R, Deghmane AE, Santecchia I, Schaub RE, Hicham S, Moya Nilges M, Malosse C, Chamot-Rooke J, Haouz A, Dillard JP, Robins WP, Taha MK, Gomperts Boneca I. Defective lytic transglycosylase disrupts cell morphogenesis by hindering cell wall de- O-acetylation in Neisseria meningitidis. eLife 2020; 9:e51247. [PMID: 32022687 PMCID: PMC7083599 DOI: 10.7554/elife.51247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/04/2020] [Indexed: 12/17/2022] Open
Abstract
Lytic transglycosylases (LT) are enzymes involved in peptidoglycan (PG) remodeling. However, their contribution to cell-wall-modifying complexes and their potential as antimicrobial drug targets remains unclear. Here, we determined a high-resolution structure of the LT, an outer membrane lipoprotein from Neisseria species with a disordered active site helix (alpha helix 30). We show that deletion of the conserved alpha-helix 30 interferes with the integrity of the cell wall, disrupts cell division, cell separation, and impairs the fitness of the human pathogen Neisseria meningitidis during infection. Additionally, deletion of alpha-helix 30 results in hyperacetylated PG, suggesting this LtgA variant affects the function of the PG de-O-acetylase (Ape 1). Our study revealed that Ape 1 requires LtgA for optimal function, demonstrating that LTs can modulate the activity of their protein-binding partner. We show that targeting specific domains in LTs can be lethal, which opens the possibility that LTs are useful drug-targets.
Collapse
Affiliation(s)
- Allison Hillary Williams
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015ParisFrance
| | - Richard Wheeler
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015ParisFrance
- Tumour Immunology and Immunotherapy, Institut Gustave RoussyVillejuifFrance
| | | | - Ignacio Santecchia
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015ParisFrance
- Universté Paris Descartes, Sorbonne Paris CitéParisFrance
| | - Ryan E Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - Samia Hicham
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015ParisFrance
| | - Maryse Moya Nilges
- Unité Technologie et Service BioImagerie Ultrastructural, Institut PasteurParisFrance
| | - Christian Malosse
- Unité Technologie et Service Spectrométrie de Masse pour la Biologie, Institut Pasteur; UMR 3528, CNRS 75015ParisFrance
| | - Julia Chamot-Rooke
- Unité Technologie et Service Spectrométrie de Masse pour la Biologie, Institut Pasteur; UMR 3528, CNRS 75015ParisFrance
| | - Ahmed Haouz
- Plate-forme de Cristallographie-C2RT, Institut Pasteur; UMR3528, CNRS 75015ParisFrance
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - William P Robins
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | | | - Ivo Gomperts Boneca
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015ParisFrance
| |
Collapse
|
4
|
Jenkins CH, Wallis R, Allcock N, Barnes KB, Richards MI, Auty JM, Galyov EE, Harding SV, Mukamolova GV. The lytic transglycosylase, LtgG, controls cell morphology and virulence in Burkholderia pseudomallei. Sci Rep 2019; 9:11060. [PMID: 31363151 PMCID: PMC6667503 DOI: 10.1038/s41598-019-47483-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of the tropical disease melioidosis. Its genome encodes an arsenal of virulence factors that allow it, when required, to switch from a soil dwelling bacterium to a deadly intracellular pathogen. With a high intrinsic resistance to antibiotics and the ability to overcome challenges from the host immune system, there is an increasing requirement for new antibiotics and a greater understanding into the molecular mechanisms of B. pseudomallei virulence and dormancy. The peptidoglycan remodeling enzymes, lytic transglycosylases (Ltgs) are potential targets for such new antibiotics. Ltgs cleave the glycosidic bonds within bacterial peptidoglycan allowing for the insertion of peptidoglycan precursors during cell growth and division, and cell membrane spanning structures such as flagella and secretion systems. Using bioinformatic analysis we have identified 8 putative Ltgs in B. pseudomallei K96243. We aimed to investigate one of these Ltgs, LtgG (BPSL3046) through the generation of deletion mutants and biochemical analysis. We have shown that LtgG is a key contributor to cellular morphology, division, motility and virulence in BALB/c mice. We have determined the crystal structure of LtgG and have identified various amino acids likely to be important in peptidoglycan binding and catalytic activity. Recombinant protein assays and complementation studies using LtgG containing a site directed mutation in aspartate 343, confirmed the essentiality of this amino acid in the function of LtgG.
Collapse
Affiliation(s)
- Christopher H Jenkins
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK.
| | - Russell Wallis
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
- The Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Natalie Allcock
- Electron Microscopy Facility, Core Biotechnology Services, University of Leicester, Leicester, UK
| | - Kay B Barnes
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK
| | - Mark I Richards
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK
| | - Joss M Auty
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Edouard E Galyov
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Galina V Mukamolova
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.
- Department of Respiratory Sciences, University of Leicester, Leicester, UK.
| |
Collapse
|
5
|
Dik DA, Batuecas MT, Lee M, Mahasenan KV, Marous DR, Lastochkin E, Fisher JF, Hermoso JA, Mobashery S. A Structural Dissection of the Active Site of the Lytic Transglycosylase MltE from Escherichia coli. Biochemistry 2018; 57:6090-6098. [PMID: 30256085 DOI: 10.1021/acs.biochem.8b00800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lytic transglycosylases (LTs) are bacterial enzymes that catalyze the cleavage of the glycan strands of the bacterial cell wall. The mechanism of this cleavage is a remarkable intramolecular transacetalization reaction, accomplished by an ensemble of active-site residues. Because the LT reaction occurs in parallel with the cell wall bond-forming reactions catalyzed by the penicillin-binding proteins, simultaneous inhibition of both enzymes can be particularly bactericidal to Gram-negative bacteria. The MltE lytic transglycosylase is the smallest of the eight LTs encoded by the Escherichia coli genome. Prior crystallographic and computational studies identified four active-site residues-E64, S73, S75, and Y192-as playing roles in catalysis. Each of these four residues was individually altered by mutation to give four variant enzymes (E64Q, S73A, S75A, and Y192F). All four variants showed reduced catalytic activity [soluble wild type (100%) > soluble Y192F and S75A (both 40%) > S73A (4%) > E64Q (≤1%)]. The crystal structure of each variant protein was determined at the resolution of 2.12 Å for E64Q, 2.33 Å for Y192F, 1.38 Å for S73A, and 1.35 Å for S75A. These variants show alteration of the hydrogen-bond interactions of the active site. Within the framework of a prior computational study of the LT mechanism, we suggest the mechanistic role of these four active-site residues in MltE catalysis.
Collapse
Affiliation(s)
- David A Dik
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - María T Batuecas
- Department of Crystallography and Structural Biology , Inst. Química-Física "Rocasolano", CSIC , Serrano 119 , 28006 Madrid , Spain
| | - Mijoon Lee
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Daniel R Marous
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Jed F Fisher
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology , Inst. Química-Física "Rocasolano", CSIC , Serrano 119 , 28006 Madrid , Spain
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| |
Collapse
|
6
|
Antibiotic Targets in Gonococcal Cell Wall Metabolism. Antibiotics (Basel) 2018; 7:antibiotics7030064. [PMID: 30037076 PMCID: PMC6164560 DOI: 10.3390/antibiotics7030064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/19/2018] [Accepted: 07/19/2018] [Indexed: 12/14/2022] Open
Abstract
The peptidoglycan cell wall that encloses the bacterial cell and provides structural support and protection is remodeled by multiple enzymes that synthesize and cleave the polymer during growth. This essential and dynamic structure has been targeted by multiple antibiotics to treat gonococcal infections. Up until now, antibiotics have been used against the biosynthetic machinery and the therapeutic potential of inhibiting enzymatic activities involved in peptidoglycan breakdown has not been explored. Given the major antibiotic resistance problems we currently face, it is crucial to identify other possible targets that are key to maintaining cell integrity and contribute to disease development. This article reviews peptidoglycan as an antibiotic target, how N. gonorrhoeae has developed resistance to currently available antibiotics, and the potential of continuing to target this essential structure to combat gonococcal infections by attacking alternative enzymatic activities involved in cell wall modification and metabolism.
Collapse
|
7
|
Vijayaraghavan J, Kumar V, Krishnan NP, Kaufhold RT, Zeng X, Lin J, van den Akker F. Structural studies and molecular dynamics simulations suggest a processive mechanism of exolytic lytic transglycosylase from Campylobacter jejuni. PLoS One 2018; 13:e0197136. [PMID: 29758058 PMCID: PMC5951611 DOI: 10.1371/journal.pone.0197136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/26/2018] [Indexed: 11/21/2022] Open
Abstract
The bacterial soluble lytic transglycosylase (LT) breaks down the peptidoglycan (PG) layer during processes such as cell division. We present here crystal structures of the soluble LT Cj0843 from Campylobacter jejuni with and without bulgecin A inhibitor in the active site. Cj0843 has a doughnut shape similar but not identical to that of E. coli SLT70. The C-terminal catalytic domain is preceded by an L-domain, a large helical U-domain, a flexible linker, and a small N-terminal NU-domain. The flexible linker allows the NU-domain to reach over and complete the circular shape, using residues conserved in the Epsilonproteobacteria LT family. The inner surface of the Cj0843 doughnut is mostly positively charged including a pocket that has 8 Arg/Lys residues. Molecular dynamics simulations with PG strands revealed a potential functional role for this pocket in anchoring the negatively charged terminal tetrapeptide of the PG during several steps in the reaction including homing and aligning the PG strand for exolytic cleavage, and subsequent ratcheting of the PG strand to enhance processivity in degrading PG strands.
Collapse
Affiliation(s)
- Jagamya Vijayaraghavan
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States of America
| | - Vijay Kumar
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States of America
| | - Nikhil P. Krishnan
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States of America
| | - Ross T. Kaufhold
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States of America
| | - Ximin Zeng
- Institute of agriculture, University of Tennessee, Knoxville, TN, United States of America
| | - Jun Lin
- Institute of agriculture, University of Tennessee, Knoxville, TN, United States of America
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States of America
- * E-mail:
| |
Collapse
|
8
|
Williams AH, Wheeler R, Rateau L, Malosse C, Chamot-Rooke J, Haouz A, Taha MK, Boneca IG. A step-by-step in crystallo guide to bond cleavage and 1,6-anhydro-sugar product synthesis by a peptidoglycan-degrading lytic transglycosylase. J Biol Chem 2018; 293:6000-6010. [PMID: 29483188 DOI: 10.1074/jbc.ra117.001095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/12/2018] [Indexed: 01/13/2023] Open
Abstract
Lytic transglycosylases (LTs) are a class of enzymes important for the recycling and metabolism of peptidoglycan (PG). LTs cleave the β-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and GlcNAc in the PG glycan strand, resulting in the concomitant formation of 1,6-anhydro-N-acetylmuramic acid and GlcNAc. No LTs reported to date have utilized chitins as substrates, despite the fact that chitins are GlcNAc polymers linked via β-1,4-glycosidic bonds, which are the known site of chemical activity for LTs. Here, we demonstrate enzymatically that LtgA, a non-canonical, substrate-permissive LT from Neisseria meningitidis utilizes chitopentaose ((GlcNAc)5) as a substrate to produce three newly identified sugars: 1,6-anhydro-chitobiose, 1,6-anhydro-chitotriose, and 1,6-anhydro-chitotetraose. Although LTs have been widely studied, their complex reactions have not previously been visualized in the crystalline state because macromolecular PG is insoluble. Here, we visualized the cleavage of the glycosidic bond and the liberation of GlcNAc-derived residues by LtgA, followed by the synthesis of atypical 1,6-anhydro-GlcNAc derivatives. In addition to the newly identified anhydro-chitin products, we identified trapped intermediates, unpredicted substrate rearrangements, sugar distortions, and a conserved crystallographic water molecule bound to the catalytic glutamate of a high-resolution native LT. This study enabled us to propose a revised alternative mechanism for LtgA that could also be applicable to other LTs. Our work contributes to the understanding of the mechanisms of LTs in bacterial cell wall biology.
Collapse
Affiliation(s)
- Allison H Williams
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, .,INSERM, 75015 Paris, France
| | - Richard Wheeler
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France.,INSERM, 75015 Paris, France.,the Gustave Roussy Comprehensive Cancer Center, Tumour Immunology and Immunotherapy, F-94805 Villejuif, France
| | - Lesly Rateau
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France.,INSERM, 75015 Paris, France
| | - Christian Malosse
- the Institut Pasteur, CNRS USR 2000, Unité des Spectrométrie de Masse Structurale et Proteomique, 75015 Paris, France
| | - Julia Chamot-Rooke
- the Institut Pasteur, CNRS USR 2000, Unité des Spectrométrie de Masse Structurale et Proteomique, 75015 Paris, France
| | - Ahmed Haouz
- the Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR3528, 75724 Paris, France, and
| | - Muhamed-Kheir Taha
- the Institut Pasteur, Département d'Infection et Epidémiologie, Unité des Infection Bactériennes Invasives, 75015 Paris, France
| | - Ivo Gomperts Boneca
- From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, .,INSERM, 75015 Paris, France
| |
Collapse
|
9
|
Dik DA, Marous DR, Fisher JF, Mobashery S. Lytic transglycosylases: concinnity in concision of the bacterial cell wall. Crit Rev Biochem Mol Biol 2017. [PMID: 28644060 DOI: 10.1080/10409238.2017.1337705] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores. Significant advances in the mechanistic understanding of each of these processes have coincided with the successive discovery of new LTs structures. In this review, we provide a systematic perspective on what is known on the structure-function correlations for the LTs, while simultaneously identifying numerous opportunities for the future study of these enigmatic enzymes.
Collapse
Affiliation(s)
- David A Dik
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Daniel R Marous
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Jed F Fisher
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Shahriar Mobashery
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| |
Collapse
|
10
|
Bulgecin A: The Key to a Broad-Spectrum Inhibitor That Targets Lytic Transglycosylases. Antibiotics (Basel) 2017; 6:antibiotics6010008. [PMID: 28241458 PMCID: PMC5372988 DOI: 10.3390/antibiotics6010008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/13/2017] [Indexed: 12/30/2022] Open
Abstract
Lytic transglycosylases (Lts) are involved in recycling, cell division, and metabolism of the peptidoglycan. They have been understudied for their usefulness as potential antibacterial targets due to their high redundancy in Gram-negative bacteria. Bulgecin A is an O-sulphonated glycopeptide that targets primarily soluble lytic tranglycosylases (Slt). It has been shown that bulgecin A increases the efficacy of β-lactams that target penicillin bindings proteins (PBPs). Here, we present the high-resolution crystal structure of LtgA from Neisseria meningitidis strain MC58, a membrane bound homolog of Escherichia coli Slt, in complex with bulgecin A. The LtgA-bulgecin A complex reveals the mechanism of inhibition by bulgecin A at near atomic resolution. We further demonstrate that bulgecin A is not only a potent inhibitor of LtgA, but most importantly, it restores the efficacy of β-lactam antibiotics in strains of N. meningitidis and Neisseria gonorrhoeae that have reduced susceptibility to β-lactams. This is particularly relevant for N. gonorrhoeae where no vaccines are available. This work illustrates how best to target dangerous pathogens using a multiple drug target approach, a new and alternative approach to fighting antibiotic resistance.
Collapse
|
11
|
Nikitushkin VD, Demina GR, Kaprelyants AS. Rpf proteins are the factors of reactivation of the dormant forms of actinobacteria. BIOCHEMISTRY (MOSCOW) 2017; 81:1719-1734. [DOI: 10.1134/s0006297916130095] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Li C, Zhu S, Tong X, Ou C, Wang LX. A facile synthesis of a complex type N-glycan thiazoline as an effective inhibitor against the antibody-deactivating endo-β-N-acetylglucosaminidases. J Carbohydr Chem 2017; 36:336-346. [PMID: 30930529 DOI: 10.1080/07328303.2017.1403616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Endo-β-N-acetylglucosaminidases are a class of endoglycosidases that deglycosylate N-glycans from glycoproteins. We describe here a facile synthesis of a complex type N-glycan thiazoline as a new mechanism-based inhibitor for this class of enzymes. The synthesis started with the readily available sialoglycopeptide (SGP) and its conversion into the glycan thiazoline through several enzymatic and chemical reactions. The synthetic glycan thiazoline showed potent inhibitory activity against several endoglycosidases including the two antibody-deactivating enzymes, Endo-S and Endo-S2, from human pathogen Streptococcus pyogenes, which would be useful as tools for structural and functional studies of these enzymes.
Collapse
Affiliation(s)
- Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, USA
| | - Shilei Zhu
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, USA
| | - Xin Tong
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, USA
| | - Chong Ou
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, USA
| |
Collapse
|
13
|
Pseudomonas aeruginosa: targeting cell-wall metabolism for new antibacterial discovery and development. Future Med Chem 2016; 8:975-92. [PMID: 27228070 DOI: 10.4155/fmc-2016-0017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas aeruginosa is a leading cause of hospital-acquired infections and is resistant to most antibiotics. With therapeutic options against P. aeruginosa dwindling, and the lack of new antibiotics in advanced developmental stages, strategies for preserving the effectiveness of current antibiotics are urgently required. β-Lactam antibiotics are important agents for treating P. aeruginosa infections, thus, adjuvants that potentiate the activity of these compounds are desirable for extending their lifespan while new antibiotics - or antibiotic classes - are discovered and developed. In this review, we discuss recent research that has identified exploitable targets of cell-wall metabolism for the design and development of compounds that hinder resistance and potentiate the activity of antipseudomonal β-lactams.
Collapse
|
14
|
Herlihey FA, Clarke AJ. Controlling Autolysis During Flagella Insertion in Gram-Negative Bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:41-56. [PMID: 27722959 DOI: 10.1007/5584_2016_52] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The flagellum is an important macromolecular machine for many pathogenic bacteria. It is a hetero-oligomeric structure comprised of three major sub-structures: basal body, hook and thin helical filament. An important step during flagellum assembly is the localized and controlled degradation of the peptidoglycan sacculus to allow for the insertion of the rod as well as to facilitate anchoring for proper motor function. The peptidoglycan lysis events require specialized lytic enzymes, β-N-acetylglucosaminidases and lytic transglycosylases, which differ in flagellated proteobacteria. Due to their autolytic activity, these enzymes need to be controlled in order to prevent cellular lysis. This review summarizes are current understanding of the peptidoglycan lysis events required for flagellum assembly and motility with a main focus on Gram-negative bacteria.
Collapse
Affiliation(s)
- Francesca A Herlihey
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada.
| |
Collapse
|
15
|
Substrate recognition and catalysis by LytB, a pneumococcal peptidoglycan hydrolase involved in virulence. Sci Rep 2015; 5:16198. [PMID: 26537571 PMCID: PMC4633669 DOI: 10.1038/srep16198] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/12/2015] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is a major cause of life-threatening diseases worldwide. Here we provide an in-depth functional characterization of LytB, the peptidoglycan hydrolase responsible for physical separation of daughter cells. Identified herein as an N-acetylglucosaminidase, LytB is involved also in colonization and invasion of the nasopharynx, biofilm formation and evasion of host immunity as previously demonstrated. We have shown that LytB cleaves the GlcNAc-β-(1,4)-MurNAc glycosidic bond of peptidoglycan building units. The hydrolysis occurs at sites with fully acetylated GlcNAc moieties, with preference for uncross-linked muropeptides. The necessity of GlcN acetylation and the presence of a single acidic moiety (Glu585) essential for catalysis strongly suggest a substrate-assisted mechanism with anchimeric assistance of the acetamido group of GlcNAc moieties. Additionally, modelling of the catalytic region bound to a hexasaccharide tripentapeptide provided insights into substrate-binding subsites and peptidoglycan recognition. Besides, cell-wall digestion products and solubilisation rates might indicate a tight control of LytB activity to prevent unrestrained breakdown of the cell wall. Choline-independent localization at the poles of the cell, mediated by the choline-binding domain, peptidoglycan modification, and choline-mediated (lipo)teichoic-acid attachment contribute to the high selectivity of LytB. Moreover, so far unknown chitin hydrolase and glycosyltransferase activities were detected using GlcNAc oligomers as substrate.
Collapse
|
16
|
Delso I, Valero-González J, Marca E, Tejero T, Hurtado-Guerrero R, Merino P. Rational Design of Glycomimetic Compounds Targeting the Saccharomyces cerevisiae Transglycosylase Gas2. Chem Biol Drug Des 2015; 87:163-70. [PMID: 26280762 DOI: 10.1111/cbdd.12650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/01/2015] [Accepted: 08/11/2015] [Indexed: 12/27/2022]
Abstract
The transglycosylase Saccharomyces cerevisiae Gas2 (ScGas2) belongs to a large family of enzymes that are key players in yeast cell wall remodeling. Despite its biologic importance, no studies on the synthesis of substrate-based compounds as potential inhibitors have been reported. We have synthesized a series of docking-guided glycomimetics that were evaluated by fluorescence spectroscopy and saturation-transfer difference (STD) NMR experiments, revealing that a minimum of three glucose units linked via a β-(1,3) linkage are required for achieving molecular recognition at the binding donor site. The binding mode of our compounds is further supported by STD-NMR experiments using the active site-mutants Y107Q and Y244Q. Our results are important for both understanding of ScGas2-substrate interactions and setting up the basis for future design of glycomimetics as new antifungal agents.
Collapse
Affiliation(s)
- Ignacio Delso
- Laboratorio de Síntesis Asimétrica, Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC, Universidad de Zaragoza, Zaragoza, Aragón, 50009, Spain.,Servicio de Resonancia Magnética Nuclear, Centro de Química y Materiales de Aragón (CEQMA), CSIC, Universidad de Zaragoza, Campus San Francisco, Zaragoza, Aragón, 50009, Spain
| | - Jessika Valero-González
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Aragón, 50009, Spain
| | - Eduardo Marca
- Laboratorio de Síntesis Asimétrica, Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC, Universidad de Zaragoza, Zaragoza, Aragón, 50009, Spain
| | - Tomás Tejero
- Laboratorio de Síntesis Asimétrica, Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC, Universidad de Zaragoza, Zaragoza, Aragón, 50009, Spain
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Aragón, 50009, Spain.,Fundación ARAID, Gobierno de Aragón, Zaragoza, Aragón 50009, Spain
| | - Pedro Merino
- Laboratorio de Síntesis Asimétrica, Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC, Universidad de Zaragoza, Zaragoza, Aragón, 50009, Spain
| |
Collapse
|
17
|
Herlihey FA, Moynihan PJ, Clarke AJ. The essential protein for bacterial flagella formation FlgJ functions as a β-N-acetylglucosaminidase. J Biol Chem 2014; 289:31029-42. [PMID: 25248745 DOI: 10.1074/jbc.m114.603944] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The flagellum is a major virulence factor of motile pathogenic bacteria. This structure requires more than 50 proteins for its biogenesis and function, one of which is FlgJ. Homologs of FlgJ produced by the β- and γ-proteobacteria, such as Salmonella enterica, Vibrio spp., and both Sphingomonas sp. and Pseudomonas spp. are bifunctional, possessing an N-terminal domain responsible for proper rod assembly and a C-terminal domain possessing peptidoglycan lytic activity. Despite the amount of research conducted on FlgJ from these and other bacteria over the past 15 years, no biochemical analysis had been conducted on any FlgJ and consequently confusion exists as to whether the enzyme is a peptidoglycan hydrolase or a lytic transglycosylase. In this study, we present the development of a novel assay for glycoside lytic enzymes and its use to provide the first enzymatic characterization of the lytic domain of FlgJ from S. enterica as the model enzyme. Surprisingly, FlgJ functions as neither a muramidase nor a lytic transglycosylases but rather as a β-N-acetylglucosaminidase. As such, FlgJ represents the first autolysin with this activity to be characterized from a Gram-negative bacterium. At its optimal pH of 4.0, the Michaelis-Menten parameters of K(m) and k(cat) for FlgJ from S. enterica were determined to be 0.64 ± 0.18 mg ml(-1) and 0.13 ± 0.016 s(-1), respectively, using purified PG as substrate. Its catalytic residues were identified as Glu(184) and Glu(223).
Collapse
Affiliation(s)
- Francesca A Herlihey
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Patrick J Moynihan
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Anthony J Clarke
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
18
|
Kuhn H, Gutelius D, Black E, Nadolny C, Basu A, Reid C. Anti-bacterial glycosyl triazoles - Identification of an N-acetylglucosamine derivative with bacteriostatic activity against Bacillus. MEDCHEMCOMM 2014; 5:1213-1217. [PMID: 25431647 PMCID: PMC4241850 DOI: 10.1039/c4md00127c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-acetylglucosaminidases (GlcNAcases) play an important role in the remodeling and recycling of bacterial peptidoglycan. Inhibitors of bacterial GlcNAcases can serve as antibacterial agents and provide an opportunity for the development of new antibiotics. We report the synthesis of triazole derivatives of N-acetylglucosamine using a copper promoted azide-alkyne coupling reaction between 1-azido-N-acetylglucosamine and a small library of terminal alkynes prepared via the Ugi reaction. These compounds were evaluated for their ability to inhibit the growth of bacteria. Two compounds that show bacteriostatic activity against Bacillus were identified, with MIC values of approximately 60 μM in both cases. Bacillus subtilis cultured in the presence of sub-MIC amounts of the glycosyl triazole inhibitors exhibit an elongated phenotype characteristic of impaired cell division. This represents the first report of inhibitors of bacterial cell wall GlcNAcases that demonstrate inhibition of cell growth in whole cell assays.
Collapse
Affiliation(s)
| | | | - Eimear Black
- Department of Chemistry, Brown University, Providence RI 02912; Department of Science and Technology, Bryant University, Providence RI 02917
| | - Christina Nadolny
- Department of Chemistry, Brown University, Providence RI 02912; Department of Science and Technology, Bryant University, Providence RI 02917
| | - Amit Basu
- Department of Chemistry, Brown University, Providence RI 02912; Department of Science and Technology, Bryant University, Providence RI 02917
| | - Christopher Reid
- Department of Chemistry, Brown University, Providence RI 02912; Department of Science and Technology, Bryant University, Providence RI 02917
| |
Collapse
|
19
|
Zeng X, Lin J. Beta-lactamase induction and cell wall metabolism in Gram-negative bacteria. Front Microbiol 2013; 4:128. [PMID: 23734147 PMCID: PMC3660660 DOI: 10.3389/fmicb.2013.00128] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/04/2013] [Indexed: 11/13/2022] Open
Abstract
Production of beta-lactamases, the enzymes that degrade beta-lactam antibiotics, is the most widespread and threatening mechanism of antibiotic resistance. In the past, extensive research has focused on the structure, function, and ecology of beta-lactamases while limited efforts were placed on the regulatory mechanisms of beta-lactamases. Recently, increasing evidence demonstrate a direct link between beta-lactamase induction and cell wall metabolism in Gram-negative bacteria. Specifically, expression of beta-lactamase could be induced by the liberated murein fragments, such as muropeptides. This article summarizes current knowledge on cell wall metabolism, beta-lactam antibiotics, and beta-lactamases. In particular, we comprehensively reviewed recent studies on the beta-lactamase induction by muropeptides via two major molecular mechanisms (the AmpG-AmpR-AmpC pathway and BlrAB-like two-component regulatory system) in Gram-negative bacteria. The signaling pathways for beta-lactamase induction offer a broad array of promising targets for the discovery of new antibacterial drugs used for combination therapies. Therefore, to develop effective mitigation strategies against the widespread beta-lactam resistance, examination of the molecular basis of beta-lactamase induction by cell wall fragment is highly warranted.
Collapse
Affiliation(s)
| | - Jun Lin
- Department of Animal Science, The University of TennesseeKnoxville, TN, USA
| |
Collapse
|
20
|
Wang JT, Lin TC, Chen YH, Lin CH, Fang JM. Polyhydroxylated pyrrolidine and 2-oxapyrrolizidine as glycosidase inhibitors. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00033h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
21
|
Abstract
Many Gram-negative and Gram-positive bacteria recycle a significant proportion of the peptidoglycan components of their cell walls during their growth and septation. In many--and quite possibly all--bacteria, the peptidoglycan fragments are recovered and recycled. Although cell-wall recycling is beneficial for the recovery of resources, it also serves as a mechanism to detect cell-wall-targeting antibiotics and to regulate resistance mechanisms. In several Gram-negative pathogens, anhydro-MurNAc-peptide cell-wall fragments regulate AmpC β-lactamase induction. In some Gram-positive organisms, short peptides derived from the cell wall regulate the induction of both β-lactamase and β-lactam-resistant penicillin-binding proteins. The involvement of peptidoglycan recycling with resistance regulation suggests that inhibitors of the enzymes involved in the recycling might synergize with cell-wall-targeted antibiotics. Indeed, such inhibitors improve the potency of β-lactams in vitro against inducible AmpC β-lactamase-producing bacteria. We describe the key steps of cell-wall remodeling and recycling, the regulation of resistance mechanisms by cell-wall recycling, and recent advances toward the discovery of cell-wall-recycling inhibitors.
Collapse
Affiliation(s)
- Jarrod W Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | | |
Collapse
|
22
|
Fibriansah G, Gliubich FI, Thunnissen AMWH. On the Mechanism of Peptidoglycan Binding and Cleavage by the endo-Specific Lytic Transglycosylase MltE from Escherichia coli. Biochemistry 2012; 51:9164-77. [DOI: 10.1021/bi300900t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Guntur Fibriansah
- Laboratory
of Biophysical Chemistry, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Francesca I. Gliubich
- Laboratory
of Biophysical Chemistry, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Laboratory
of Biophysical Chemistry, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| |
Collapse
|
23
|
Abstract
The review summarizes the abundant information on the 35 identified peptidoglycan (PG) hydrolases of Escherichia coli classified into 12 distinct families, including mainly glycosidases, peptidases, and amidases. An attempt is also made to critically assess their functions in PG maturation, turnover, elongation, septation, and recycling as well as in cell autolysis. There is at least one hydrolytic activity for each bond linking PG components, and most hydrolase genes were identified. Few hydrolases appear to be individually essential. The crystal structures and reaction mechanisms of certain hydrolases having defined functions were investigated. However, our knowledge of the biochemical properties of most hydrolases still remains fragmentary, and that of their cellular functions remains elusive. Owing to redundancy, PG hydrolases far outnumber the enzymes of PG biosynthesis. The presence of the two sets of enzymes acting on the PG bonds raises the question of their functional correlations. It is difficult to understand why E. coli keeps such a large set of PG hydrolases. The subtle differences in substrate specificities between the isoenzymes of each family certainly reflect a variety of as-yet-unidentified physiological functions. Their study will be a far more difficult challenge than that of the steps of the PG biosynthesis pathway.
Collapse
Affiliation(s)
- Jean van Heijenoort
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Bat 430, Université Paris-Sud, Orsay F-91405, France.
| |
Collapse
|
24
|
Georgelis N, Tabuchi A, Nikolaidis N, Cosgrove DJ. Structure-function analysis of the bacterial expansin EXLX1. J Biol Chem 2011; 286:16814-23. [PMID: 21454649 DOI: 10.1074/jbc.m111.225037] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We made use of EXLX1, an expansin from Bacillus subtilis, to investigate protein features essential for its plant cell wall binding and wall loosening activities. We found that the two expansin domains, D1 and D2, need to be linked for wall extension activity and that D2 mediates EXLX1 binding to whole cell walls and to cellulose via distinct residues on the D2 surface. Binding to cellulose is mediated by three aromatic residues arranged linearly on the putative binding surface that spans D1 and D2. Mutation of these three residues to alanine eliminated cellulose binding and concomitantly eliminated wall loosening activity measured either by cell wall extension or by weakening of filter paper but hardly affected binding to whole cell walls, which is mediated by basic residues located on other D2 surfaces. Mutation of these basic residues to glutamine reduced cell wall binding but not wall loosening activities. We propose domain D2 as the founding member of a new carbohydrate binding module family, CBM63, but its function in expansin activity apparently goes beyond simply anchoring D1 to the wall. Several polar residues on the putative binding surface of domain D1 are also important for activity, most notably Asp82, whose mutation to alanine or asparagine completely eliminated wall loosening activity. The functional insights based on this bacterial expansin may be extrapolated to the interactions of plant expansins with cell walls.
Collapse
Affiliation(s)
- Nikolaos Georgelis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | | | | |
Collapse
|
25
|
Characterization of peptidoglycan hydrolase in Cag pathogenicity island of Helicobacter pylori. Mol Biol Rep 2010; 38:503-9. [PMID: 20358296 DOI: 10.1007/s11033-010-0134-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 03/23/2010] [Indexed: 10/19/2022]
Abstract
The Cag Type IV secretion apparatus proteins in Helicobacter pylori can mediate the injection of effector CagA protein into eukaryotic target cells. Although this apparatus forms an important pathway for bacterium-host interaction, its assembly process in vivo is poorly understood, and the proteins which contribute to break the bacterial cell walls in Cag-PAI have not yet been identified. The cagγ gene in Cag-PAI is a unique member that contains a conserved SLT catalysis domain, which makes it an attracting question whether cagy gene has the capacity to digest the bacterial cell wall. In the current study, therefore, the cagγ gene was cloned from the H. pylori NCTC 11637 and expressed in Escherichia coli, and its lytic effect on cell walls in vitro was observed. Results indicated that Cagγ protein has a lytic activity against bacterial cell walls. An allelic-exchange mutant (Δcagγ) was further constructed to investigate the relationship between Cagγ and effector CagA translocation. These results suggested that Cagγ contributed to the assembly of Cag Type IV secretion apparatus by digesting the peptidoglycan meshwork of bacterial cell walls.
Collapse
|
26
|
Demina GR, Makarov VA, Nikitushkin VD, Ryabova OB, Vostroknutova GN, Salina EG, Shleeva MO, Goncharenko AV, Kaprelyants AS. Finding of the low molecular weight inhibitors of resuscitation promoting factor enzymatic and resuscitation activity. PLoS One 2009; 4:e8174. [PMID: 20016836 PMCID: PMC2790607 DOI: 10.1371/journal.pone.0008174] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 11/08/2009] [Indexed: 11/19/2022] Open
Abstract
Background Resuscitation promoting factors (RPF) are secreted proteins involved in reactivation of dormant actinobacteria, including Mycobacterium tuberculosis. They have been considered as prospective targets for the development of new anti-tuberculosis drugs preventing reactivation of dormant tubercle bacilli, generally associated with latent tuberculosis. However, no inhibitors of Rpf activity have been reported so far. The goal of this study was to find low molecular weight compounds inhibiting the enzymatic and biological activities of Rpfs. Methodology/Principal Findings Here we describe a novel class of 2-nitrophenylthiocyanates (NPT) compounds that inhibit muralytic activity of Rpfs with IC50 1–7 µg/ml. Fluorescence studies revealed interaction of active NPTs with the internal regions of the Rpf molecule. Candidate inhibitors of Rpf enzymatic activity showed a bacteriostatic effect on growth of Micrococcus luteus (in which Rpf is essential for growth protein) at concentrations close to IC50. The candidate compounds suppressed resuscitation of dormant (“non-culturable”) cells of M. smegmatis at 1 µg/ml or delayed resuscitation of dormant M. tuberculosis obtained in laboratory conditions at 10 µg/ml. However, they did not inhibit growth of active mycobacteria under these concentrations. Conclusions/Significance NPT are the first example of low molecular weight compounds that inhibit the enzymatic and biological activities of Rpf proteins.
Collapse
|
27
|
Simple construction of fused and spiro nitrogen/sulfur containing heterocycles by addition of thioamides or thioureas on cycloalkenyl-diazenes: examples of click chemistry. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.01.102] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
28
|
Li B, Takegawa K, Suzuki T, Yamamoto K, Wang LX. Synthesis and inhibitory activity of oligosaccharide thiazolines as a class of mechanism-based inhibitors for endo-beta-N-acetylglucosaminidases. Bioorg Med Chem 2008; 16:4670-5. [PMID: 18304822 DOI: 10.1016/j.bmc.2008.02.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 02/05/2008] [Accepted: 02/08/2008] [Indexed: 11/16/2022]
Abstract
A facile synthesis of oligosaccharide-thiazoline derivatives of N-glycans as a novel class of inhibitors for endo-beta-N-acetylglucosaminidases was described. It was found that the external sugar residues on the N-glycan core could enhance the inhibitory potency. While the Manbeta1,4GlcNAc- and Man3GlcNAc-thiazolines were only moderate inhibitors, the large Man9GlcNAc-thiazoline demonstrated potent inhibitory activity, with an IC(50) of 0.22 and 0.42 microM against the Arthrobacter enzyme (Endo-A) and the human endo-beta-N-acetylglycosaminidase (hENGase), respectively. It was also observed that the oligosaccharide thiazolines could differentially inhibit endo-beta-N-acetylglucosaminidases from different sources. These oligosaccharide thiazolines represent the first class of endo-beta-N-acetylglucosaminidase inhibitors.
Collapse
Affiliation(s)
- Bing Li
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | | | | | | |
Collapse
|
29
|
Vollmer W, Joris B, Charlier P, Foster S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol Rev 2008; 32:259-86. [PMID: 18266855 DOI: 10.1111/j.1574-6976.2007.00099.x] [Citation(s) in RCA: 609] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Most bacteria have multiple peptidoglycan hydrolases capable of cleaving covalent bonds in peptidoglycan sacculi or its fragments. An overview of the different classes of peptidoglycan hydrolases and their cleavage sites is provided. The physiological functions of these enzymes include the regulation of cell wall growth, the turnover of peptidoglycan during growth, the separation of daughter cells during cell division and autolysis. Specialized hydrolases enlarge the pores in the peptidoglycan for the assembly of large trans-envelope complexes (pili, flagella, secretion systems), or they specifically cleave peptidoglycan during sporulation or spore germination. Moreover, peptidoglycan hydrolases are involved in lysis phenomena such as fratricide or developmental lysis occurring in bacterial populations. We will also review the current view on the regulation of autolysins and on the role of cytoplasm hydrolases in peptidoglycan recycling and induction of beta-lactamase.
Collapse
Affiliation(s)
- Waldemar Vollmer
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne, UK.
| | | | | | | |
Collapse
|
30
|
Scheurwater E, Reid CW, Clarke AJ. Lytic transglycosylases: Bacterial space-making autolysins. Int J Biochem Cell Biol 2008; 40:586-91. [PMID: 17468031 DOI: 10.1016/j.biocel.2007.03.018] [Citation(s) in RCA: 225] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 03/20/2007] [Accepted: 03/21/2007] [Indexed: 11/29/2022]
Abstract
Lytic transglycosylases are an important class of bacterial enzymes that act on peptidoglycan with the same substrate specificity as lysozyme. Unlike the latter enzymes, however, the lytic transglycosylases are not hydrolases but instead cleave the glycosidic linkage between N-actetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anydromuramoyl product. They are ubiquitous in bacteria which produce a compliment of different forms that are responsible for creating space within the peptidoglycan sacculus for its biosynthesis and recycling, cell division, and the insertion of cell-envelope spanning structures, such as flagella and secretion systems. As well, the lytic transglyosylases may have a role in pathogenesis of some bacterial species. Given their important role in bacterial cell wall metabolism, the lytic transglycosylases may present an attractive new target for the development of broad-spectrum antibiotics.
Collapse
Affiliation(s)
- Edie Scheurwater
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | |
Collapse
|
31
|
Reid CW, Legaree BA, Clarke AJ. Role of Ser216 in the mechanism of action of membrane-bound lytic transglycosylase B: Further evidence for substrate-assisted catalysis. FEBS Lett 2007; 581:4988-92. [PMID: 17910958 DOI: 10.1016/j.febslet.2007.09.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Accepted: 09/19/2007] [Indexed: 11/21/2022]
Abstract
Lytic transglycosylases cleave the beta-(1-->4)-glycosidic bond in the bacterial cell wall heteropolymer peptidoglycan between the N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues with the concomitant formation of a 1,6-anhydromuramoyl residue. Based on sequence alignments, Ser216 in Pseudomonas aeruginosa membrane-bound lytic transglycosylase B (MltB) was targeted for replacement with alanine to delineate its role in the enzyme's mechanism of action. The specific activity of the Ser216-->Ala MltB derivative was less than 12% of that for the wild-type enzyme, while its substrate binding affinity remained virtually unaltered. These data are in agreement with a role of Ser216 in orienting the N-acetyl group on MurNAc at the -1 subsite of MltB for its participation in a substrate-assisted mechanism of action.
Collapse
Affiliation(s)
- Christopher W Reid
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | | |
Collapse
|
32
|
van Straaten KE, Barends TRM, Dijkstra BW, Thunnissen AMWH. Structure of Escherichia coli Lytic Transglycosylase MltA with Bound Chitohexaose. J Biol Chem 2007; 282:21197-205. [PMID: 17502382 DOI: 10.1074/jbc.m701818200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Crystal structures of an inactive mutant (D308A) of the lytic transglycosylase MltA from Escherichia coli have been determined in two different apo-forms, as well as in complex with the substrate analogue chitohexaose. The chitohexaose binds with all six saccharide residues in the active site groove, with an intact glycosidic bond at the bond cleavage center. Its binding induces a large reorientation of the two structural domains in MltA, narrowing the active site groove and allowing tight interactions of the oligosaccharide with residues from both domains. The structures identify residues in MltA with key roles in the binding and recognition of peptidoglycan and confirm that Asp-308 is the single catalytic residue, acting as a general acid/base. Moreover, the structures suggest that catalysis involves a high energy conformation of the scissile glycosidic linkage and that the putative oxocarbenium ion intermediate is stabilized by the dipole moment of a nearby alpha-helix.
Collapse
Affiliation(s)
- Karin E van Straaten
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | | | | |
Collapse
|
33
|
Miroshnikov KA, Faizullina NM, Sykilinda NN, Mesyanzhinov VV. Properties of the endolytic transglycosylase encoded by gene 144 of Pseudomonas aeruginosa bacteriophage phiKZ. BIOCHEMISTRY (MOSCOW) 2006; 71:300-5. [PMID: 16545067 DOI: 10.1134/s0006297906030102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteriophage endolysins degrading bacterial cell walls are prospective enzymes for therapy of bacterial infections. The genome of the giant bacteriophage phiKZ of Pseudomonas aeruginosa encodes two endolysins, gene products (g.p.) 144 and 181, which are homologous to lytic transglycosylases. Gene 144 encoding a 260 amino acid residue protein was cloned into the plasmid expression vector. Recombinant g.p. 144 purified from Escherichia coli effectively degrades chloroform-treated P. aeruginosa cell walls. The protein has predominantly alpha-helical conformation and exists in solution in stoichiometric monomer : dimer : trimer equilibrium. Antibodies against the protein bind the phage particle. This demonstrates that g.p. 144 is a structural component of the phiKZ particle, presumably, a phage tail.
Collapse
Affiliation(s)
- K A Miroshnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow.
| | | | | | | |
Collapse
|
34
|
Zahrl D, Wagner M, Bischof K, Bayer M, Zavecz B, Beranek A, Ruckenstuhl C, Zarfel GE, Koraimann G. Peptidoglycan degradation by specialized lytic transglycosylases associated with type III and type IV secretion systems. Microbiology (Reading) 2005; 151:3455-3467. [PMID: 16272370 DOI: 10.1099/mic.0.28141-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Specialized lytic transglycosylases are muramidases capable of locally degrading the peptidoglycan meshwork of Gram-negative bacteria. Specialized lytic transglycosylase genes are present in clusters encoding diverse macromolecular transport systems. This paper reports the analysis of selected members of the specialized lytic transglycosylase family from type III and type IV secretion systems. These proteins were analysedin vivoby assaying their ability to complement the DNA transfer defect of the conjugative F-like plasmid R1-16 lacking a functional P19 protein, the specialized lytic transglycosylase of this type IV secretion system. Heterologous complementation was accomplished using IpgF from the plasmid-encoded type III secretion system ofShigella sonneiand TrbN from the type IV secretion system of the conjugative plasmid RP4. In contrast, neither VirB1 proteins (Agrobacterium tumefaciens,Brucella suis) nor IagB (Salmonella enterica) could functionally replace P19.In vitro, IpgF, IagB, both VirB1 proteins, HP0523 (Helicobacter pylori) and P19 displayed peptidoglycanase activity in zymogram analyses. Using an established test system and a newly developed assay it was shown that IpgF degraded peptidoglycan in solution. IpgF was active only after removal of the chaperonin GroEL, which co-purified with IpgF and inhibited its enzymic activity. A mutant IpgF protein in which the predicted catalytic amino acid, Glu42, was replaced by Gln, was completely inactive. IpgF-catalysed peptidoglycan degradation was optimal at pH 6 and was inhibited by the lytic transglycosylase inhibitors hexa-N-acetylchitohexaose and bulgecin A.
Collapse
Affiliation(s)
- Doris Zahrl
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Maria Wagner
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Karin Bischof
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Michaela Bayer
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Barbara Zavecz
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Andreas Beranek
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Christoph Ruckenstuhl
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Gernot E Zarfel
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Günther Koraimann
- Institut für Molekulare Biowissenschaften (IMB), Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
| |
Collapse
|
35
|
Abstract
The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.
Collapse
Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
| | | |
Collapse
|