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Jasilionis A, Plotka M, Wang L, Dorawa S, Lange J, Watzlawick H, van den Bergh T, Vroling B, Altenbuchner J, Kaczorowska AK, Pohl E, Kaczorowski T, Nordberg Karlsson E, Freitag-Pohl S. AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase. Protein Sci 2023; 32:e4585. [PMID: 36721347 PMCID: PMC9929850 DOI: 10.1002/pro.4585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
Bacteriophages encode a wide variety of cell wall disrupting enzymes that aid the viral escape in the final stages of infection. These lytic enzymes have accumulated notable interest due to their potential as novel antibacterials for infection treatment caused by multiple-drug resistant bacteria. Here, the detailed functional and structural characterization of Thermus parvatiensis prophage peptidoglycan lytic amidase AmiP, a globular Amidase_3 type lytic enzyme adapted to high temperatures is presented. The sequence and structure comparison with homologous lytic amidases reveals the key adaptation traits that ensure the activity and stability of AmiP at high temperatures. The crystal structure determined at a resolution of 1.8 Å displays a compact α/β-fold with multiple secondary structure elements omitted or shortened compared with protein structures of similar proteins. The functional characterization of AmiP demonstrates high efficiency of catalytic activity and broad substrate specificity toward thermophilic and mesophilic bacteria strains containing Orn-type or DAP-type peptidoglycan. The here presented AmiP constitutes the most thermoactive and ultrathermostable Amidase_3 type lytic enzyme biochemically characterized with a temperature optimum at 85°C. The extraordinary high melting temperature Tm 102.6°C confirms fold stability up to approximately 100°C. Furthermore, AmiP is shown to be more active over the alkaline pH range with pH optimum at pH 8.5 and tolerates NaCl up to 300 mM with the activity optimum at 25 mM NaCl. This set of beneficial characteristics suggests that AmiP can be further exploited in biotechnology.
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Affiliation(s)
- Andrius Jasilionis
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Lei Wang
- Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | | | | | | | - Josef Altenbuchner
- Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Ehmke Pohl
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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Metal cofactor stabilization by a partner protein is a widespread strategy employed for amidase activation. Proc Natl Acad Sci U S A 2022; 119:e2201141119. [PMID: 35733252 PMCID: PMC9245657 DOI: 10.1073/pnas.2201141119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Construction and remodeling of the bacterial peptidoglycan (PG) cell wall must be carefully coordinated with cell growth and division. Central to cell wall construction are hydrolases that cleave bonds in peptidoglycan. These enzymes also represent potential new antibiotic targets. One such hydrolase, the amidase LytH in Staphylococcus aureus, acts to remove stem peptides from PG, controlling where substrates are available for insertion of new PG strands and consequently regulating cell size. When it is absent, cells grow excessively large and have division defects. For activity, LytH requires a protein partner, ActH, that consists of an intracellular domain, a large rhomboid protease domain, and three extracellular tetratricopeptide repeats (TPRs). Here, we demonstrate that the amidase-activating function of ActH is entirely contained in its extracellular TPRs. We show that ActH binding stabilizes metals in the LytH active site and that LytH metal binding in turn is needed for stable complexation with ActH. We further present a structure of a complex of the extracellular domains of LytH and ActH. Our findings suggest that metal cofactor stabilization is a general strategy used by amidase activators and that ActH houses multiple functions within a single protein.
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3
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Nöldeke ER, Stehle T. Unraveling the mechanism of peptidoglycan amidation by the bifunctional enzyme complex GatD/MurT: A comparative structural approach. Int J Med Microbiol 2019; 309:151334. [PMID: 31383542 DOI: 10.1016/j.ijmm.2019.151334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022] Open
Abstract
The bacterial cell wall provides structural integrity to the cell and protects the cell from internal pressure and the external environment. During the course of the twelve-year funding period of the Collaborative Research Center 766, our work has focused on conducting structure-function studies of enzymes that modify (synthesize or cleave) cell wall components of a range of bacteria including Staphylococcus aureus, Staphylococcus epidermidis, and Nostoc punctiforme. Several of our structures represent promising targets for interference. In this review, we highlight a recent structure-function analysis of an enzyme complex that is responsible for the amidation of Lipid II, a peptidoglycan precursor, in S. aureus.
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Affiliation(s)
- Erik R Nöldeke
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076 Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076 Tübingen, Germany; Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
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4
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Discovery and Biochemical Characterization of PlyP56, PlyN74, and PlyTB40- Bacillus Specific Endolysins. Viruses 2018; 10:v10050276. [PMID: 29883383 PMCID: PMC5977269 DOI: 10.3390/v10050276] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 12/27/2022] Open
Abstract
Three Bacillus bacteriophage-derived endolysins, designated PlyP56, PlyN74, and PlyTB40, were identified, cloned, purified, and characterized for their antimicrobial properties. Sequence alignment reveals these endolysins have an N-terminal enzymatically active domain (EAD) linked to a C-terminal cell wall binding domain (CBD). PlyP56 has a Peptidase_M15_4/VanY superfamily EAD with a conserved metal binding motif and displays biological dependence on divalent ions for activity. In contrast, PlyN74 and PlyTB40 have T7 lysozyme-type Amidase_2 and carboxypeptidase T-type Amidase_3 EADs, respectively, which are members of the MurNAc-LAA superfamily, but are not homologs and thus do not have a shared protein fold. All three endolysins contain similar SH3-family CBDs. Although minor host range differences were noted, all three endolysins show relatively broad antimicrobial activity against members of the Bacillus cereus sensu lato group with the highest lytic activity against B. cereus ATCC 4342. Characterization studies determined the optimal lytic activity for these enzymes was at physiological pH (pH 7.0–8.0), over a broad temperature range (4–55 °C), and at low concentrations of NaCl (<50 mM). Direct comparison of lytic activity shows the PlyP56 enzyme to be twice as effective at lysing the cell wall peptidoglycan as PlyN74 or PlyTB40, suggesting PlyP56 is a good candidate for further antimicrobial development as well as bioengineering studies.
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Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases. Curr Opin Struct Biol 2017; 44:87-100. [PMID: 28109980 DOI: 10.1016/j.sbi.2017.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/23/2016] [Accepted: 01/02/2017] [Indexed: 01/26/2023]
Abstract
The major component of bacterial cell wall is peptidoglycan (PG), a complex polymer formed by long glycan chains cross-linked by peptide stems. PG is in constant equilibrium requiring well-orchestrated coordination between synthesis and degradation. The resulting cell-wall fragments can be recycled, act as messengers for bacterial communication, as effector molecules in immune response or as signaling molecules triggering antibiotics resistance. Tailoring and recycling of PG requires the cleavage of different covalent bonds of the PG sacculi by a diverse set of specific enzymes whose activities are strictly regulated. Here, we review the molecular mechanisms that govern PG remodeling focusing on the structural information available for the bacterial lytic enzymes and the mechanisms by which they recognize their substrates.
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Domínguez-Gil T, Lee M, Acebrón-Avalos I, Mahasenan KV, Hesek D, Dik DA, Byun B, Lastochkin E, Fisher JF, Mobashery S, Hermoso JA. Activation by Allostery in Cell-Wall Remodeling by a Modular Membrane-Bound Lytic Transglycosylase from Pseudomonas aeruginosa. Structure 2016; 24:1729-1741. [PMID: 27618662 DOI: 10.1016/j.str.2016.07.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 11/19/2022]
Abstract
Bacteria grow and divide without loss of cellular integrity. This accomplishment is notable, as a key component of their cell envelope is a surrounding glycopeptide polymer. In Gram-negative bacteria this polymer-the peptidoglycan-grows by the difference between concurrent synthesis and degradation. The regulation of the enzymatic ensemble for these activities is poorly understood. We report herein the structural basis for the control of one such enzyme, the lytic transglycosylase MltF of Pseudomonas aeruginosa. Its structure comprises two modules: an ABC-transporter-like regulatory module and a catalytic module. Occupancy of the regulatory module by peptidoglycan-derived muropeptides effects a dramatic and long-distance (40 Å) conformational change, occurring over the entire protein structure, to open its active site for catalysis. This discovery of the molecular basis for the allosteric control of MltF catalysis is foundational to further study of MltF within the complex enzymatic orchestration of the dynamic peptidoglycan.
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Affiliation(s)
- Teresa Domínguez-Gil
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Iván Acebrón-Avalos
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - David A Dik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Byungjin Byun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Juan A Hermoso
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
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Domínguez-Gil T, Molina R, Alcorlo M, Hermoso JA. Renew or die: The molecular mechanisms of peptidoglycan recycling and antibiotic resistance in Gram-negative pathogens. Drug Resist Updat 2016; 28:91-104. [PMID: 27620957 DOI: 10.1016/j.drup.2016.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance is one of the most serious health threats. Cell-wall remodeling processes are tightly regulated to warrant bacterial survival and in some cases are directly linked to antibiotic resistance. Remodeling produces cell-wall fragments that are recycled but can also act as messengers for bacterial communication, as effector molecules in immune response and as signaling molecules triggering antibiotic resistance. This review is intended to provide state-of-the-art information about the molecular mechanisms governing this process and gather structural information of the different macromolecular machineries involved in peptidoglycan recycling in Gram-negative bacteria. The growing body of literature on the 3D structures of the corresponding macromolecules reveals an extraordinary complexity. Considering the increasing incidence and widespread emergence of Gram-negative multidrug-resistant pathogens in clinics, structural information on the main actors of the recycling process paves the way for designing novel antibiotics disrupting cellular communication in the recycling-resistance pathway.
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Affiliation(s)
- Teresa Domínguez-Gil
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Martín Alcorlo
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
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8
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Sandalova T, Lee M, Henriques-Normark B, Hesek D, Mobashery S, Mellroth P, Achour A. The crystal structure of the major pneumococcal autolysin LytA in complex with a large peptidoglycan fragment reveals the pivotal role of glycans for lytic activity. Mol Microbiol 2016; 101:954-67. [PMID: 27273793 DOI: 10.1111/mmi.13435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 12/18/2022]
Abstract
The pneumococcal autolysin LytA is a key virulence factor involved in several important functions including DNA competence, immune evasion and biofilm formation. Here, we present the 1.05 Å crystal structure of the catalytic domain of LytA in complex with a synthetic cell-wall-based peptidoglycan (PG) ligand that occupies the entire Y-shaped substrate-binding crevice. As many as twenty-one amino-acid residues are engaged in ligand interactions with a majority of these interactions directed towards the glycan strand. All saccharides are intimately bound through hydrogen bond, van der Waals and CH-π interactions. Importantly, the structure of LytA is not altered upon ligand binding, whereas the bound ligand assumes a different conformation compared to the unbound NMR-based solution structure of the same PG-fragment. Mutational study reveals that several non-catalytic glycan-interacting residues, structurally conserved in other amidases from Gram-positive Firmicutes, are pivotal for enzymatic activity. The three-dimensional structure of the LytA/PG complex provides a novel structural basis for ligand restriction by the pneumococcal autolysin, revealing for the first time an importance of the multivalent binding to PG saccharides.
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Affiliation(s)
- Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Department of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, SE, 17176, Sweden
| | - Mijoon Lee
- Departments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, 17176, Sweden
| | - Dusan Hesek
- Departments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Shahriar Mobashery
- Departments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Peter Mellroth
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden. .,Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, 17176, Sweden.
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Department of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, SE, 17176, Sweden.
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Büttner FM, Faulhaber K, Forchhammer K, Maldener I, Stehle T. Enabling cell-cell communication via nanopore formation: structure, function and localization of the unique cell wall amidase AmiC2 of Nostoc punctiforme. FEBS J 2016; 283:1336-50. [PMID: 26833702 DOI: 10.1111/febs.13673] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/07/2016] [Accepted: 01/27/2016] [Indexed: 01/14/2023]
Abstract
UNLABELLED To orchestrate a complex life style in changing environments, the filamentous cyanobacterium Nostoc punctiforme facilitates communication between neighboring cells through septal junction complexes. This is achieved by nanopores that perforate the peptidoglycan (PGN) layer and traverse the cell septa. The N-acetylmuramoyl-l-alanine amidase AmiC2 (Npun_F1846; EC 3.5.1.28) in N. punctiforme generates arrays of such nanopores in the septal PGN, in contrast to homologous amidases that mediate daughter cell separation after cell division in unicellular bacteria. Nanopore formation is therefore a novel property of AmiC homologs. Immunofluorescence shows that native AmiC2 localizes to the maturing septum. The high-resolution crystal structure (1.12 Å) of its catalytic domain (AmiC2-cat) differs significantly from known structures of cell splitting and PGN recycling amidases. A wide and shallow binding cavity allows easy access of the substrate to the active site, which harbors an essential zinc ion. AmiC2-cat exhibits strong hydrolytic activity in vitro. A single point mutation of a conserved glutamate near the zinc ion results in total loss of activity, whereas zinc removal leads to instability of AmiC2-cat. An inhibitory α-helix, as found in the Escherichia coli AmiC(E. coli) structure, is absent. Taken together, our data provide insight into the cell-biological, biochemical and structural properties of an unusual cell wall lytic enzyme that generates nanopores for cell-cell communication in multicellular cyanobacteria. The novel structural features of the catalytic domain and the unique biological function of AmiC2 hint at mechanisms of action and regulation that are distinct from other amidases. DATABASE The AmiC2-cat structure has been deposited in the Protein Data Bank under accession number 5EMI.
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Affiliation(s)
- Felix M Büttner
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Katharina Faulhaber
- Interfaculty Institute for Microbiology and Infection Medicine, Department of Organismic Interactions, University of Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Department of Organismic Interactions, University of Tübingen, Germany
| | - Iris Maldener
- Interfaculty Institute for Microbiology and Infection Medicine, Department of Organismic Interactions, University of Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany.,Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
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10
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Braun V, Götz F, Schultz JE, Wohlleben W. The bacterial cell envelope: structure, function, and infection interface. Int J Med Microbiol 2014; 305:175-7. [PMID: 25660413 DOI: 10.1016/j.ijmm.2014.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Volkmar Braun
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Tübingen, Germany
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
| | - Joachim E Schultz
- Pharmazeutische Biochemie, Pharmazeutisches Institut, University of Tübingen, Germany
| | - Wolfgang Wohlleben
- Biotechnology/Microbiology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany.
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