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Pantiora PD, Georgakis ND, Premetis GE, Labrou NE. Metagenomic analysis of hot spring soil for mining a novel thermostable enzybiotic. Appl Microbiol Biotechnol 2024; 108:163. [PMID: 38252132 PMCID: PMC10803476 DOI: 10.1007/s00253-023-12979-2] [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: 08/17/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024]
Abstract
The misuse and overuse of antibiotics have contributed to a rapid emergence of antibiotic-resistant bacterial pathogens. This global health threat underlines the urgent need for innovative and novel antimicrobials. Endolysins derived from bacteriophages or prophages constitute promising new antimicrobials (so-called enzybiotics), exhibiting the ability to break down bacterial peptidoglycan (PG). In the present work, metagenomic analysis of soil samples, collected from thermal springs, allowed the identification of a prophage-derived endolysin that belongs to the N-acetylmuramoyl-L-alanine amidase type 2 (NALAA-2) family and possesses a LysM (lysin motif) region as a cell wall binding domain (CWBD). The enzyme (Ami1) was cloned and expressed in Escherichia coli, and its bactericidal and lytic activity was characterized. The results indicate that Ami1 exhibits strong bactericidal and antimicrobial activity against a broad range of bacterial pathogens, as well as against isolated peptidoglycan (PG). Among the examined bacterial pathogens, Ami1 showed highest bactericidal activity against Staphylococcus aureus sand Staphylococcus epidermidis cells. Thermostability analysis revealed a melting temperature of 64.2 ± 0.6 °C. Overall, these findings support the potential that Ami1, as a broad spectrum antimicrobial agent, could be further assessed as enzybiotic for the effective treatment of bacterial infections. KEY POINTS: • Metagenomic analysis allowed the identification of a novel prophage endolysin • The endolysin belongs to type 2 amidase family with lysin motif region • The endolysin displays high thermostability and broad bactericidal spectrum.
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Affiliation(s)
- Panagiota D Pantiora
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nikolaos D Georgakis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Georgios E Premetis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece.
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2
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Induction of AmpC-Mediated β-Lactam Resistance Requires a Single Lytic Transglycosylase in Agrobacterium tumefaciens. Appl Environ Microbiol 2022; 88:e0033322. [PMID: 35638841 PMCID: PMC9238390 DOI: 10.1128/aem.00333-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The remarkable ability of Agrobacterium tumefaciens to transfer DNA to plant cells has allowed the generation of important transgenic crops. One challenge of A. tumefaciens-mediated transformation is eliminating the bacteria after plant transformation to prevent detrimental effects to plants and the release of engineered bacteria to the environment. Here, we use a reverse-genetics approach to identify genes involved in ampicillin resistance, with the goal of utilizing these antibiotic-sensitive strains for plant transformations. We show that treating A. tumefaciens C58 with ampicillin led to increased β-lactamase production, a response dependent on the broad-spectrum β-lactamase AmpC and its transcription factor, AmpR. Loss of the putative ampD orthologue atu2113 led to constitutive production of AmpC-dependent β-lactamase activity and ampicillin resistance. Finally, one cell wall remodeling enzyme, MltB3, was necessary for the AmpC-dependent β-lactamase activity, and its loss elicited ampicillin and carbenicillin sensitivity in the A. tumefaciens C58 and GV3101 strains. Furthermore, GV3101 ΔmltB3 transforms plants with efficiency comparable to that of the wild type but can be cleared with sublethal concentrations of ampicillin. The functional characterization of the genes involved in the inducible ampicillin resistance pathway of A. tumefaciens constitutes a major step forward in efforts to reduce the intrinsic antibiotic resistance of this bacterium. IMPORTANCE Agrobacterium tumefaciens, a significant biotechnological tool for production of transgenic plant lines, is highly resistant to a wide variety of antibiotics, posing challenges for various applications. One challenge is the efficient elimination of A. tumefaciens from transformed plant tissue without using levels of antibiotics that are toxic to the plants. Here, we present the functional characterization of genes involved in β-lactam resistance in A. tumefaciens. Knowledge about proteins that promote or inhibit β-lactam resistance will enable the development of strains to improve the efficiency of Agrobacterium-mediated plant genetic transformations. Effective removal of Agrobacterium from transformed plant tissue has the potential to maximize crop yield and food production, improving the outlook for global food security.
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Sekiya H, Kamitori S, Nariya H, Matsunami R, Tamai E. Structural and biochemical characterization of the Clostridium perfringens-specific Zn 2+-dependent amidase endolysin, Psa, catalytic domain. Biochem Biophys Res Commun 2021; 576:66-72. [PMID: 34482025 DOI: 10.1016/j.bbrc.2021.08.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/27/2021] [Indexed: 11/19/2022]
Abstract
Phage-derived endolysins, enzymes that degrade peptidoglycans, have the potential to serve as alternative antimicrobial agents. Psa, which was identified as an endolysin encoded in the genome of Clostridium perfringens st13, was shown to specifically lyse C. perfringens. Psa has an N-terminal catalytic domain that is homologous to the Amidase_2 domain (PF01510), and a novel C-terminal cell wall-binding domain. Here, we determined the X-ray structure of the Psa catalytic domain (Psa-CD) at 1.65 Å resolution. Psa-CD has a typical Amidase_2 domain structure, consisting of a spherical structure with a central β-sheet surrounded by two α-helix groups. Furthermore, there is a Zn2+ at the center of Psa-CD catalytic reaction site, as well as a unique T-shaped substrate-binding groove consisting of two grooves on the molecule surface. We performed modeling study of the enzyme/substrate complex along with a mutational analysis, and demonstrated that the structure of the substrate-binding groove is closely related to the amidase activity. Furthermore, we proposed a Zn2+-mediated catalytic reaction mechanism for the Amidase_2 family, in which tyrosine constitutes part of the catalytic reaction site.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Hirofumi Nariya
- Laboratory of Food Microbiology, Graduate School of Human Life Sciences Food and Nutritional Sciences, Jumonji University, 2-1-28, Kansawa, Niiza, Saitama, 352-8510, Japan
| | - Risa Matsunami
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan; Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
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A Putative Amidase Endolysin Encoded by Clostridium perfringens St13 Exhibits Specific Lytic Activity and Synergizes with the Muramidase Endolysin Psm. Antibiotics (Basel) 2021; 10:antibiotics10030245. [PMID: 33804492 PMCID: PMC7999503 DOI: 10.3390/antibiotics10030245] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 01/21/2023] Open
Abstract
Clostridium perfringens is an often-harmful intestinal bacterium that causes various diseases ranging from food poisoning to life-threatening fulminant disease. Potential treatments include phage-derived endolysins, a promising family of alternative antimicrobial agents. We surveyed the genome of the C. perfringens st13 strain and identified an endolysin gene, psa, in the phage remnant region. Psa has an N-terminal catalytic domain that is homologous to the amidase_2 domain, and a C-terminal domain of unknown function. psa and gene derivatives encoding various Psa subdomains were cloned and expressed in Escherichia coli as N-terminal histidine-tagged proteins. Purified His-tagged full-length Psa protein (Psa-his) showed C. perfringens-specific lytic activity in turbidity reduction assays. In addition, we demonstrated that the uncharacterized C-terminal domain has cell wall-binding activity. Furthermore, cell wall-binding measurements showed that Psa binding was highly specific to C. perfringens. These results indicated that Psa is an amidase endolysin that specifically lyses C. perfringens; the enzyme’s specificity is highly dependent on the binding of the C-terminal domain. Moreover, Psa was shown to have a synergistic effect with another C. perfringens-specific endolysin, Psm, which is a muramidase that cleaves peptidoglycan at a site distinct from that targeted by Psa. The combination of Psa and Psm may be effective in the treatment and prevention of C. perfringens infections.
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Zellner B, Mengin-Lecreulx D, Tully B, Gunning WT, Booth R, Huntley JF. A Francisella tularensis L,D-carboxypeptidase plays important roles in cell morphology, envelope integrity, and virulence. Mol Microbiol 2021; 115:1357-1378. [PMID: 33469978 DOI: 10.1111/mmi.14685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
Francisella tularensis is a Gram-negative, intracellular bacterium that causes the zoonotic disease tularemia. Intracellular pathogens, including F. tularensis, have evolved mechanisms to survive in the harsh environment of macrophages and neutrophils, where they are exposed to cell envelope-damaging molecules. The bacterial cell wall, primarily composed of peptidoglycan (PG), maintains cell morphology, structure, and membrane integrity. Intracellular Gram-negative bacteria protect themselves from macrophage and neutrophil killing by recycling and repairing damaged PG--a process that involves over 50 different PG synthesis and recycling enzymes. Here, we identified a PG recycling enzyme, L,D-carboxypeptidase A (LdcA), of F. tularensis that is responsible for converting PG tetrapeptide stems to tripeptide stems. Unlike E. coli LdcA and most other orthologs, F. tularensis LdcA does not localize to the cytoplasm and also exhibits L,D-endopeptidase activity, converting PG pentapeptide stems to tripeptide stems. Loss of F. tularensis LdcA led to altered cell morphology and membrane integrity, as well as attenuation in a mouse pulmonary infection model and in primary and immortalized macrophages. Finally, an F. tularensis ldcA mutant protected mice against virulent Type A F. tularensis SchuS4 pulmonary challenge.
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Affiliation(s)
- Briana Zellner
- Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH, USA
| | - Dominique Mengin-Lecreulx
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Brenden Tully
- Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH, USA
| | | | - Robert Booth
- Department of Pathology, University of Toledo, Toledo, OH, USA
| | - Jason F Huntley
- Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH, USA
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Delvaux C, Dauvin M, Boulanger M, Quinton L, Mengin-Lecreulx D, Joris B, Pauw ED, Far J. Use of Capillary Zone Electrophoresis Coupled to Electrospray Mass Spectrometry for the Detection and Absolute Quantitation of Peptidoglycan-Derived Peptides in Bacterial Cytoplasmic Extracts. Anal Chem 2021; 93:2342-2350. [PMID: 33470796 DOI: 10.1021/acs.analchem.0c04218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptidoglycan (PGN) is an essential structure found in the bacterial cell wall. During the bacterial life cycle, PGN continuously undergoes biosynthesis and degradation to ensure bacterial growth and division. The resulting PGN fragments (muropeptides and peptides), which are generated by the bacterial autolytic system, are usually transported into the cytoplasm to be recycled. On the other hand, PGN fragments can act as messenger molecules involved in the bacterial cell wall stress response as in the case of β-lactamase induction in the presence of β-lactam antibiotic or in triggering mammalian innate immune response. During their cellular life, bacteria modulate their PGN degradation by their autolytic system or their recognition by the mammalian innate immune system by chemically modifying their PGN. Among these modifications, the amidation of the ε-carboxyl group of meso-diaminopimelic acid present in the PGN peptide chain is frequently observed. Currently, the detection and quantitation of PGN-derived peptides is still challenging because of the difficulty in separating these highly hydrophilic molecules by RP-HPLC as these compounds are eluted closely after the column void volume or coeluted in many cases. Here, we report the use of capillary zone electrophoresis coupled via an electrospray-based CE-MS interface to high-resolution mass spectrometry for the quantitation of three PGN peptides of interest and their amidated derivatives in bacterial cytoplasmic extracts. The absolute quantitation of the tripeptide based on the [13C,15N] isotopically labeled standard was also performed in crude cytoplasmic extracts of bacteria grown in the presence or absence of a β-lactam antibiotic (cephalosporin C). Despite the high complexity of the samples, the repeatability of the CZE-MS quantitation results was excellent, with relative standard deviations close to 1%. The global reproducibility of the method including biological handling was better than 20%.
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Affiliation(s)
- Cédric Delvaux
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Marjorie Dauvin
- Centre for Protein Engineering, InBioS Research Unit, Quartier Agora, University of Liège, Allée du Six Août 13, B-4000 Liège, Belgium
| | - Madeleine Boulanger
- Centre for Protein Engineering, InBioS Research Unit, Quartier Agora, University of Liège, Allée du Six Août 13, B-4000 Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Dominique Mengin-Lecreulx
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Bernard Joris
- Centre for Protein Engineering, InBioS Research Unit, Quartier Agora, University of Liège, Allée du Six Août 13, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
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Vermassen A, Leroy S, Talon R, Provot C, Popowska M, Desvaux M. Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan. Front Microbiol 2019; 10:331. [PMID: 30873139 PMCID: PMC6403190 DOI: 10.3389/fmicb.2019.00331] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/08/2019] [Indexed: 11/13/2022] Open
Abstract
The cell wall (CW) of bacteria is an intricate arrangement of macromolecules, at least constituted of peptidoglycan (PG) but also of (lipo)teichoic acids, various polysaccharides, polyglutamate and/or proteins. During bacterial growth and division, there is a constant balance between CW degradation and biosynthesis. The CW is remodeled by bacterial hydrolases, whose activities are carefully regulated to maintain cell integrity or lead to bacterial death. Each cell wall hydrolase (CWH) has a specific role regarding the PG: (i) cell wall amidase (CWA) cleaves the amide bond between N-acetylmuramic acid and L-alanine residue at the N-terminal of the stem peptide, (ii) cell wall glycosidase (CWG) catalyses the hydrolysis of the glycosidic linkages, whereas (iii) cell wall peptidase (CWP) cleaves amide bonds between amino acids within the PG chain. After an exhaustive overview of all known conserved catalytic domains responsible for CWA, CWG, and CWP activities, this review stresses that the CWHs frequently display a modular architecture combining multiple and/or different catalytic domains, including some lytic transglycosylases as well as CW binding domains. From there, direct physiological and collateral roles of CWHs in bacterial cells are further discussed.
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Affiliation(s)
- Aurore Vermassen
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Régine Talon
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | | | - Magdalena Popowska
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
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Abstract
The peptidoglycan sacculus is a net-like polymer that surrounds the cytoplasmic membrane in most bacteria. It is essential to maintain the bacterial cell shape and protect from turgor. The peptidoglycan has a basic composition, common to all bacteria, with species-specific variations that can modify its biophysical properties or the pathogenicity of the bacteria. The synthesis of peptidoglycan starts in the cytoplasm and the precursor lipid II is flipped across the cytoplasmic membrane. The new peptidoglycan strands are synthesised and incorporated into the pre-existing sacculus by the coordinated activities of peptidoglycan synthases and hydrolases. In the model organism Escherichia coli there are two complexes required for the elongation and division. Each of them is regulated by different proteins from both the cytoplasmic and periplasmic sides that ensure the well-coordinated synthesis of new peptidoglycan.
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Ishida T. Antibacterial mechanism of Ag+ ions for bacteriolyses of bacterial cell walls via peptidoglycan autolysins, and DNA damages. ACTA ACUST UNITED AC 2018. [DOI: 10.15406/mojt.2018.04.00125] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Wilmes M, Meier K, Schiefer A, Josten M, Otten CF, Klöckner A, Henrichfreise B, Vollmer W, Hoerauf A, Pfarr K. AmiD Is a Novel Peptidoglycan Amidase in Wolbachia Endosymbionts of Drosophila melanogaster. Front Cell Infect Microbiol 2017; 7:353. [PMID: 28824885 PMCID: PMC5543032 DOI: 10.3389/fcimb.2017.00353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/21/2017] [Indexed: 11/13/2022] Open
Abstract
Wolbachia endobacteria are obligate intracellular bacteria with a highly reduced genome infecting many arthropod and filarial species, in which they manipulate arthropod reproduction to increase their transmission and are essential for nematode development and survival. The Wolbachia genome encodes all enzymes required for the synthesis of the cell wall building block lipid II, although a peptidoglycan-like structure has not been detected. Despite the ability to synthesize lipid II, Wolbachia from arthropods and nematodes have only a subset of genes encoding enzymes involved in the periplasmic processing of lipid II and peptidoglycan recycling, with arthropods having two more than nematodes. We functionally analyzed the activity of the putative cell wall hydrolase AmiD from the Wolbachia endosymbiont of Drosophila melanogaster, an enzyme not encoded by the nematode endobacteria. Wolbachia AmiD has Zn2+-dependent amidase activity and cleaves intact peptidoglycan, monomeric lipid II and anhydromuropeptides, substrates that are generated during bacterial growth. AmiD may have been maintained in arthropod Wolbachia to avoid host immune recognition by degrading cell wall fragments in the periplasm. This is the first description of a wolbachial lipid II processing enzyme putatively expressed in the periplasm.
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Affiliation(s)
- Miriam Wilmes
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
| | - Kirstin Meier
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
| | - Andrea Schiefer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
| | - Michaele Josten
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
| | - Christian F Otten
- Institute for Cell and Molecular Bioscience, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Anna Klöckner
- Institute for Pharmaceutical Microbiology, University of BonnBonn, Germany
| | | | - Waldemar Vollmer
- Institute for Cell and Molecular Bioscience, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-CologneBonn, Germany
| | - Kenneth Pfarr
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
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Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains. mBio 2015; 6:e02327-14. [PMID: 26374125 PMCID: PMC4600125 DOI: 10.1128/mbio.02327-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (or dl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l-Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.
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Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family. Structure 2014; 22:1799-1809. [PMID: 25465128 DOI: 10.1016/j.str.2014.09.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 01/01/2023]
Abstract
GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo structure at 1.15 Å resolution shows that AmiA is related to NlpC/P60 γ-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and subsequently were characterized experimentally. Further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines another amidase family.
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13
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Gene deletions in Mycobacterium bovis BCG stimulate increased CD8+ T cell responses. Infect Immun 2014; 82:5317-26. [PMID: 25287928 DOI: 10.1128/iai.02100-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacteria, the etiological agents of tuberculosis and leprosy, have coevolved with mammals for millions of years and have numerous ways of suppressing their host's immune response. It has been suggested that mycobacteria may contain genes that reduce the host's ability to elicit CD8(+) T cell responses. We screened 3,290 mutant Mycobacterium bovis bacillus Calmette Guerin (BCG) strains to identify genes that decrease major histocompatibility complex (MHC) class I presentation of mycobacterium-encoded epitope peptides. Through our analysis, we identified 16 mutant BCG strains that generated increased transgene product-specific CD8(+) T cell responses. The genes disrupted in these mutant strains had disparate predicted functions. Reconstruction of strains via targeted deletion of genes identified in the screen recapitulated the enhanced immunogenicity phenotype of the original mutant strains. When we introduced the simian immunodeficiency virus (SIV) gag gene into several of these novel BCG strains, we observed enhanced SIV Gag-specific CD8(+) T cell responses in vivo. This study demonstrates that mycobacteria carry numerous genes that act to dampen CD8(+) T cell responses and suggests that genetic modification of these genes may generate a novel group of recombinant BCG strains capable of serving as more effective and immunogenic vaccine vectors.
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Menanteau-Ledouble S, Lawrence ML. Use of bioluminescence mutant screening for identification of Edwardsiella ictaluri genes involved in channel catfish (Ictalurus punctatus) skin colonization. Vet Microbiol 2013; 162:724-730. [DOI: 10.1016/j.vetmic.2012.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 09/05/2012] [Accepted: 09/28/2012] [Indexed: 01/02/2023]
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Ikeda N, Karlyshev AV. Putative mechanisms and biological role of coccoid form formation in Campylobacter jejuni. Eur J Microbiol Immunol (Bp) 2012; 2:41-9. [PMID: 24611120 DOI: 10.1556/eujmi.2.2012.1.7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Accepted: 01/09/2012] [Indexed: 01/09/2023] Open
Abstract
In certain conditions Campylobacter jejuni cells are capable of changing their cell shape from a typically spiral to a coccoid form (CF). By similarity to other bacteria, the latter was initially considered to be a viable but non-culturable form capable of survival in unfavourable conditions. However, subsequent studies with C. jejuni and closely related bacteria Helicobacter pylori suggested that CF represents a non-viable, degenerative form. Until now, the issue on whether the CF of C. jejuni is viable and infective is highly controversial. Despite some preliminary experiments on characterization of CF cells, neither biochemical mechanisms nor genetic determinants involved in C. jejuni cell shape changes have been characterized. In this review, we highlight known molecular mechanisms and genes involved in CF formation in other bacteria. Since orthologous genes are also present in C. jejuni, we suggest that CF formation in these bacteria is also a regulated and genetically determined process. A possible significance of CF in the lifestyle of this important bacterial pathogen is discussed.
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Affiliation(s)
- N Ikeda
- School of Life Sciences, Faculty of Science, Engineering and Computing, Kingston University Penrhyn Road, Kingston-upon Thames, KT1 2EE UK
| | - A V Karlyshev
- School of Life Sciences, Faculty of Science, Engineering and Computing, Kingston University Penrhyn Road, Kingston-upon Thames, KT1 2EE UK
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16
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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.
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Affiliation(s)
- Jean van Heijenoort
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Bat 430, Université Paris-Sud, Orsay F-91405, France.
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17
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LysA2, the Lactobacillus casei bacteriophage A2 lysin is an endopeptidase active on a wide spectrum of lactic acid bacteria. Appl Microbiol Biotechnol 2011; 94:101-10. [DOI: 10.1007/s00253-011-3588-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 08/23/2011] [Accepted: 09/15/2011] [Indexed: 01/21/2023]
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18
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Maqbool A, Levdikov VM, Blagova EV, Hervé M, Horler RSP, Wilkinson AJ, Thomas GH. Compensating stereochemical changes allow murein tripeptide to be accommodated in a conventional peptide-binding protein. J Biol Chem 2011; 286:31512-21. [PMID: 21705338 PMCID: PMC3173086 DOI: 10.1074/jbc.m111.267179] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The oligopeptide permease (Opp) of Escherichia coli is an ATP-binding cassette transporter that uses the substrate-binding protein (SBP) OppA to bind peptides and deliver them to the membrane components (OppBCDF) for transport. OppA binds conventional peptides 2-5 residues in length regardless of their sequence, but does not facilitate transport of the cell wall component murein tripeptide (Mtp, L-Ala-γ-D-Glu-meso-Dap), which contains a D-amino acid and a γ-peptide linkage. Instead, MppA, a homologous substrate-binding protein, forms a functional transporter with OppBCDF for uptake of this unusual tripeptide. Here we have purified MppA and demonstrated biochemically that it binds Mtp with high affinity (K(D) ∼ 250 nM). The crystal structure of MppA in complex with Mtp has revealed that Mtp is bound in a relatively extended conformation with its three carboxylates projecting from one side of the molecule and its two amino groups projecting from the opposite face. Specificity for Mtp is conferred by charge-charge and dipole-charge interactions with ionic and polar residues of MppA. Comparison of the structure of MppA-Mtp with structures of conventional tripeptides bound to OppA, reveals that the peptide ligands superimpose remarkably closely given the profound differences in their structures. Strikingly, the effect of the D-stereochemistry, which projects the side chain of the D-Glu residue at position 2 in the direction of the main chain in a conventional tripeptide, is compensated by the formation of a γ-linkage to the amino group of diaminopimelic acid, mimicking the peptide bond between residues 2 and 3 of a conventional tripeptide.
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Affiliation(s)
- Abbas Maqbool
- Department of Biology (Area 10), University of York, York YO10 5YW, United Kingdom
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19
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Das D, Hervé M, Feuerhelm J, Farr CL, Chiu HJ, Elsliger MA, Knuth MW, Klock HE, Miller MD, Godzik A, Lesley SA, Deacon AM, Mengin-Lecreulx D, Wilson IA. Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein. PLoS One 2011; 6:e17624. [PMID: 21445265 PMCID: PMC3060825 DOI: 10.1371/journal.pone.0017624] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/03/2011] [Indexed: 11/18/2022] Open
Abstract
Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.
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Affiliation(s)
- Debanu Das
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Mireille Hervé
- Université Paris-Sud, Laboratoire des Enveloppes Bactériennes et Antibiotiques, Orsay, France
- Centre National de la Recherche Scientifique, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Orsay, France
| | - Julie Feuerhelm
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Carol L. Farr
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Marc-André Elsliger
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Mark W. Knuth
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Heath E. Klock
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Mitchell D. Miller
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Adam Godzik
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Center for Research in Biological Systems, University of California San Diego, La Jolla, California, United States of America
- Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Scott A. Lesley
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ashley M. Deacon
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Dominique Mengin-Lecreulx
- Université Paris-Sud, Laboratoire des Enveloppes Bactériennes et Antibiotiques, Orsay, France
- Centre National de la Recherche Scientifique, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Orsay, France
| | - Ian A. Wilson
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
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20
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Removal of l-alanine from the production of l-2-aminobutyric acid by introduction of alanine racemase and d-amino acid oxidase. Appl Microbiol Biotechnol 2011; 90:903-10. [DOI: 10.1007/s00253-011-3127-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 01/10/2011] [Accepted: 01/10/2011] [Indexed: 10/18/2022]
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21
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Mercier F, Zervosen A, Teller N, Frère JM, Herman R, Pennartz A, Joris B, Luxen A. 1,6-AnhMurNAc derivatives for assay development of amidase AmiD. Bioorg Med Chem 2010; 18:7422-31. [DOI: 10.1016/j.bmc.2010.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 08/10/2010] [Accepted: 09/02/2010] [Indexed: 10/19/2022]
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22
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Kerff F, Petrella S, Mercier F, Sauvage E, Herman R, Pennartz A, Zervosen A, Luxen A, Frère JM, Joris B, Charlier P. Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family. J Mol Biol 2009; 397:249-59. [PMID: 20036252 DOI: 10.1016/j.jmb.2009.12.038] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/15/2009] [Accepted: 12/18/2009] [Indexed: 11/16/2022]
Abstract
AmiD is the fifth identified N-acetylmuramoyl-L-alanine zinc amidase of Escherichia coli. This periplasmic lipoprotein is anchored in the outer membrane and has a broad specificity. AmiD is capable of cleaving the intact peptidoglycan (PG) as well as soluble fragments containing N-acetylmuramic acid regardless of the presence of an anhydro form or not, unlike the four other amidases, AmiA, AmiB, AmiC, and AmpD, which have some specificity. AmiD function is, however, not clearly established but it could be part of the enzymatic machinery involved in the PG turnover in E. coli. We solved three structures of the E. coli zinc amidase AmiD devoid of its lipidic anchorage: the holoenzyme, the apoenzyme in complex with the substrate anhydro-N-acetylmuramic-acid-L-Ala-gamma-d-Glu-L-Lys, and the holoenzyme in complex with the L-Ala-gamma-D-Glu-L-Lys peptide, the product of the hydrolysis of this substrate by AmiD. The AmiD structure shows a relatively flexible N-terminal extension that allows an easy reach of the PG by the enzyme inserted into the outer membrane. The C-terminal domain provides a potential extended geometrical complementarity to the substrate. AmiD shares a common fold with AmpD, the bacteriophage T7 lysozyme, and the PG recognition proteins, which are receptor proteins involved in the innate immune responses of a wide range of organisms. Analysis of the different structures reveals the similarity between the catalytic mechanism of zinc amidases of the AmiD family and the thermolysin-related zinc peptidases.
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Affiliation(s)
- Frédéric Kerff
- Centre d'Ingénierie des Protéines, University of Liège, Allée du 6 Août 17, Bât B5a, 4000 Liège, Belgium
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