51
|
Díez-Martínez R, De Paz HD, García-Fernández E, Bustamante N, Euler CW, Fischetti VA, Menendez M, García P. A novel chimeric phage lysin with high in vitro and in vivo bactericidal activity against Streptococcus pneumoniae. J Antimicrob Chemother 2015; 70:1763-73. [PMID: 25733585 DOI: 10.1093/jac/dkv038] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/29/2015] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Streptococcus pneumoniae is becoming increasingly antibiotic resistant worldwide and new antimicrobials are urgently needed. Our aim was new chimeric phage endolysins, or lysins, with improved bactericidal activity by swapping the structural components of two pneumococcal phage lysozymes: Cpl-1 (the best lysin tested to date) and Cpl-7S. METHODS The bactericidal effects of four new chimeric lysins were checked against several bacteria. The purified enzymes were added at different concentrations to resuspended bacteria and viable cells were measured after 1 h. Killing capacity of the most active lysin, Cpl-711, was tested in a mouse bacteraemia model, following mouse survival after injecting different amounts (25-500 μg) of enzyme. The capacity of Cpl-711 to reduce pneumococcal biofilm formation was also studied. RESULTS The chimera Cpl-711 substantially improved the killing activity of the parental phage lysozymes, Cpl-1 and Cpl-7S, against pneumococcal bacteria, including multiresistant strains. Specifically, 5 μg/mL Cpl-711 killed ≥7.5 log of pneumococcal R6 strain. Cpl-711 also reduced pneumococcal biofilm formation and killed 4 log of the bacterial population at 1 μg/mL. Mice challenged intraperitoneally with D39_IU pneumococcal strain were protected by treatment with a single intraperitoneal injection of Cpl-711 1 h later, resulting in about 50% greater protection than with Cpl-1. CONCLUSIONS Domain swapping among phage lysins allows the construction of new chimeric enzymes with high bactericidal activity and a different substrate range. Cpl-711, the most powerful endolysin against pneumococci, offers a promising therapeutic perspective for the treatment of multiresistant pneumococcal infections.
Collapse
Affiliation(s)
- Roberto Díez-Martínez
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, USA CIBER de Enfermedades Respiratorias, Madrid, Spain
| | - Héctor D De Paz
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Esther García-Fernández
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain CIBER de Enfermedades Respiratorias, Madrid, Spain
| | - Noemí Bustamante
- CIBER de Enfermedades Respiratorias, Madrid, Spain Departamento de Química-Física Biológica, Instituto Química-Física Rocasolano, CSIC, Madrid, Spain
| | - Chad W Euler
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, USA Department of Medical Laboratory Sciences, Hunter College, CUNY, New York, NY, USA
| | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, USA
| | - Margarita Menendez
- CIBER de Enfermedades Respiratorias, Madrid, Spain Departamento de Química-Física Biológica, Instituto Química-Física Rocasolano, CSIC, Madrid, Spain
| | - Pedro García
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain CIBER de Enfermedades Respiratorias, Madrid, Spain
| |
Collapse
|
52
|
Modulation of domain-domain interaction and protein function by a charged linker: A case study of mycobacteriophage D29 endolysin. FEBS Lett 2015; 589:695-701. [DOI: 10.1016/j.febslet.2015.01.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 01/03/2015] [Accepted: 01/30/2015] [Indexed: 11/18/2022]
|
53
|
Proença D, Velours C, Leandro C, Garcia M, Pimentel M, São-José C. A two-component, multimeric endolysin encoded by a single gene. Mol Microbiol 2014; 95:739-53. [PMID: 25388025 DOI: 10.1111/mmi.12857] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2014] [Indexed: 01/11/2023]
Abstract
Bacteriophage endolysins are bacterial cell wall degrading enzymes whose potential to fight bacterial infections has been intensively studied. Endolysins from Gram-positive systems are typically described as monomeric and as having a modular structure consisting of one or two N-terminal catalytic domains (CDs) linked to a C-terminal region responsible for cell wall binding (CWB). We show here that expression of the endolysin gene lys170 of the enterococcal phage F170/08 results in two products, the expected full length endolysin (Lys170FL) and a C-terminal fragment corresponding to the CWB domain (CWB170). The latter is produced from an in-frame, alternative translation start site. Both polypeptides interact to form the fully active endolysin. Biochemical data strongly support a model where Lys170 is made of one monomer of Lys170FL associated with up to three CWB170 subunits, which are responsible for efficient endolysin binding to its substrate. Bioinformatics analysis indicates that similar secondary translation start signals may be used to produce and add independent CWB170-like subunits to different enzymatic specificities. The particular configuration of endolysin Lys170 uncovers a new mode of increasing the number of CWB motifs associated to CD modules, as an alternative to the tandem repetition typically found in monomeric cell wall hydrolases.
Collapse
Affiliation(s)
- Daniela Proença
- Technophage, SA, Av. Professor Egas Moniz, Ed. Egas Moniz, piso 2, 1649-028, Lisboa, Portugal
| | | | | | | | | | | |
Collapse
|
54
|
Heselpoth RD, Owens JM, Nelson DC. Quantitative analysis of the thermal stability of the gamma phage endolysin PlyG: a biophysical and kinetic approach to assaying therapeutic potential. Virology 2014; 477:125-132. [PMID: 25432575 DOI: 10.1016/j.virol.2014.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/27/2014] [Accepted: 11/03/2014] [Indexed: 01/11/2023]
Abstract
Endolysins are lytic enzymes encoded by bacteriophage that represent an emerging class of protein therapeutics. Considering macromolecular thermoresistance correlates with shelf life, PlyG, a Bacillus anthracis endolysin, was thermally characterized to further evaluate its therapeutic potential. Results from a biophysical thermal analysis revealed full-length PlyG and its isolated domains comprised thermal denaturation temperatures exceeding 63°C. In the absence of reducing agent, PlyG was determined to be kinetically unstable, a finding hypothesized to be attributable to the chemical oxidation of cysteine and/or methionine residues. The presence of reducing agent kinetically stabilized the endolysin, with PlyG retaining at least ~50% residual lytic activity after being heated at temperatures up to 80°C and remaining enzymatically functional after being boiled. Furthermore, the endolysin had a kinetic half-life at 50°C and 55°C of 35 and 5.5h, respectively. PlyG represents a thermostable proteinaceous antibacterial with subsequent prolonged therapeutic shelf life expectancy.
Collapse
Affiliation(s)
- Ryan D Heselpoth
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Jacqueline M Owens
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Biotechnology Program, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Daniel C Nelson
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
55
|
Fischetti VA. Exploiting what phage have evolved to control gram-positive pathogens. BACTERIOPHAGE 2014; 1:188-194. [PMID: 23050211 PMCID: PMC3448103 DOI: 10.4161/bact.1.4.17747] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In the billion years that bacteriophage (or phage) have existed together with bacteria the phage have evolved systems that may be exploited for our benefit. One of these is the lytic system used by the phage to release their progeny from an infected bacterium. Endolysins (or lysins) are highly evolved enzymes in the lytic system produced to cleave essential bonds in the bacterial cell wall peptidoglycan for progeny release. Small quantities of purified recombinant lysin added externally to gram-positive bacteria results in immediate lysis causing log-fold death of the target bacterium. Lysins have now been used successfully in a variety of animal models to control pathogenic antibiotic resistant bacteria found on mucosal surfaces and in infected tissues. The advantages over antibiotics are their specificity for the pathogen without disturbing the normal flora, the low chance of bacterial resistance, and their ability to kill colonizing pathogens on mucosal surfaces, a capacity previously unavailable. Lysins therefore, may be a much-needed anti-infective (or enzybiotic) in an age of mounting antibiotic resistance.
Collapse
Affiliation(s)
- Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis; Rockefeller University; New York, NY USA
| |
Collapse
|
56
|
Fenton M, Cooney JC, Ross RP, Sleator RD, McAuliffe O, O'Mahony J, Coffey A. In silico modeling of the staphylococcal bacteriophage-derived peptidase CHAP(K). BACTERIOPHAGE 2014; 1:198-206. [PMID: 23050213 PMCID: PMC3448105 DOI: 10.4161/bact.1.4.18245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The aim of this study was to use comparative modeling to predict the three-dimensional structure of the CHAPK protein (cysteine, histidine-dependent amidohydrolase/peptidase domain of the LysK endolysin, derived from bacteriophage K). Iterative PSI-BLAST searches against the Protein Data Bank (PDB) and nonredundant (nr) databases were used to populate a multiple alignment for analysis using the T-Coffee Expresso server. A consensus Maximum Parsimony phylogenetic tree with a bootstrap analysis setting of 1,000 replicates was constructed using MEGA4. Structural templates relevant to our target (CHAPK) were identified, processed in Expresso and used to generate a 3D model in the alignment mode of SWISS-MODEL. These templates were also processed in the I-TASSER web server. A Staphylococcus saprophyticus CHAP domain protein, 2K3A, was identified as the structural template in both servers. The I-TASSER server generated the CHAPK model with the best bond geometries when analyzed using PROCHECK and the most logical organization of the structure. The predicted 3D model indicates that CHAPK has a papain-like fold. Circular dichroism spectropolarimetry also indicated that CHAPK has an αβ fold, which is consistent with the model presented. The putative active site maintained a highly conserved Cys54-His117-Glu134 charge relay and an oxyanion hole residue Asn136. The residue triplet, Cys-His-Glu, is known to be a viable proteolytic triad in which we predict the Cys residue is used in a nucleophilic attack on peptide bonds at a specific site in the pentaglycine cross bridge of staphylococcal cell wall peptidoglycan. Use of comparative modeling has allowed approximation of the 3D structure of CHAPK giving information on the structure and an insight into the binding and active site of the catalytic domain. This may facilitate its development as an alternative antibacterial agent.
Collapse
Affiliation(s)
- Mark Fenton
- Department of Biological Sciences; Cork Institute of Technology; Cork, Ireland
| | | | | | | | | | | | | |
Collapse
|
57
|
Yang H, Yu J, Wei H. Engineered bacteriophage lysins as novel anti-infectives. Front Microbiol 2014; 5:542. [PMID: 25360133 PMCID: PMC4199284 DOI: 10.3389/fmicb.2014.00542] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 09/29/2014] [Indexed: 12/17/2022] Open
Abstract
Bacteriophage lysins, the highly evolved specific peptidoglycan hydrolases, have long been demonstrated to be effective enzybiotics in various infectious models. The modular structure of lysins makes it possible to design bioengineered lysins that have desired properties, such as higher activity, or broader killing spectrum. Moreover, lysins can even be engineered to kill Gram-negative bacterial pathogens from without, a property that is not present in natural lysins. In this era of ever increasing multidrug resistant pathogens, engineered lysins represent a new class of enzybiotics that are powerful and readily available to fight antimicrobial resistance.
Collapse
Affiliation(s)
- Hang Yang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, China
| | - Junping Yu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, China
| |
Collapse
|
58
|
Bellinzoni M, Haouz A, Miras I, Magnet S, André-Leroux G, Mukherjee R, Shepard W, Cole ST, Alzari PM. Structural studies suggest a peptidoglycan hydrolase function for the Mycobacterium tuberculosis Tat-secreted protein Rv2525c. J Struct Biol 2014; 188:156-64. [PMID: 25260828 DOI: 10.1016/j.jsb.2014.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/08/2014] [Accepted: 09/16/2014] [Indexed: 11/18/2022]
Abstract
Among the few proteins shown to be secreted by the Tat system in Mycobacterium tuberculosis, Rv2525c is of particular interest, since its gene is conserved in the minimal genome of Mycobacterium leprae. Previous evidence linked this protein to cell wall metabolism and sensitivity to β-lactams. We describe here the crystal structure of Rv2525c that shows a TIM barrel-like fold characteristic of glycoside hydrolases of the GH25 family, which includes prokaryotic and phage-encoded peptidoglycan hydrolases. Structural comparison with other members of this family combined with substrate docking suggest that, although the 'neighbouring group' catalytic mechanism proposed for this family still appears as the most plausible, the identity of residues involved in catalysis in GH25 hydrolases might need to be revised.
Collapse
Affiliation(s)
- Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Ahmed Haouz
- Institut Pasteur, Plateforme de Cristallographie (CNRS-UMR3528), 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Isabelle Miras
- Institut Pasteur, Plateforme de Cristallographie (CNRS-UMR3528), 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Sophie Magnet
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France; Unité Mathématique, Informatique et Génome (MIG), INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
| | - Raju Mukherjee
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - William Shepard
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette Cedex, France
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| |
Collapse
|
59
|
Sabala I, Jagielska E, Bardelang PT, Czapinska H, Dahms SO, Sharpe JA, James R, Than ME, Thomas NR, Bochtler M. Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans. FEBS J 2014; 281:4112-22. [PMID: 25039253 PMCID: PMC4286107 DOI: 10.1111/febs.12929] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/23/2014] [Accepted: 07/11/2014] [Indexed: 01/29/2023]
Abstract
Staphylococcus simulans biovar staphylolyticus lysostaphin efficiently cleaves Staphylococcus aureus cell walls. The protein is in late clinical trials as a topical anti-staphylococcal agent, and can be used to prevent staphylococcal growth on artificial surfaces. Moreover, the gene has been both stably engineered into and virally delivered to mice or livestock to obtain resistance against staphylococci. Here, we report the first crystal structure of mature lysostaphin and two structures of its isolated catalytic domain at 3.5, 1.78 and 1.26 Å resolution, respectively. The structure of the mature active enzyme confirms its expected organization into catalytic and cell-wall-targeting domains. It also indicates that the domains are mobile with respect to each other because of the presence of a highly flexible peptide linker. The high-resolution structures of the catalytic domain provide details of Zn2+ coordination and may serve as a starting point for the engineering of lysostaphin variants with improved biotechnological characteristics.
Collapse
Affiliation(s)
- Izabela Sabala
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
60
|
Dunne M, Mertens HDT, Garefalaki V, Jeffries CM, Thompson A, Lemke EA, Svergun DI, Mayer MJ, Narbad A, Meijers R. The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor. PLoS Pathog 2014; 10:e1004228. [PMID: 25058163 PMCID: PMC4110038 DOI: 10.1371/journal.ppat.1004228] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 05/19/2014] [Indexed: 02/04/2023] Open
Abstract
The bacteriophage ΦCD27 is capable of lysing Clostridium difficile, a pathogenic bacterium that is a major cause for nosocomial infection. A recombinant CD27L endolysin lyses C. difficile in vitro, and represents a promising alternative as a bactericide. To better understand the lysis mechanism, we have determined the crystal structure of an autoproteolytic fragment of the CD27L endolysin. The structure covers the C-terminal domain of the endolysin, and represents a novel fold that is identified in a number of lysins that target Clostridia bacteria. The structure indicates endolysin cleavage occurs at the stem of the linker connecting the catalytic domain with the C-terminal domain. We also solved the crystal structure of the C-terminal domain of a slow cleaving mutant of the CTP1L endolysin that targets C. tyrobutyricum. Two distinct dimerization modes are observed in the crystal structures for both endolysins, despite a sequence identity of only 22% between the domains. The dimers are validated to be present for the full length protein in solution by right angle light scattering, small angle X-ray scattering and cross-linking experiments using the cross-linking amino acid p-benzoyl-L-phenylalanine (pBpa). Mutagenesis on residues contributing to the dimer interfaces indicates that there is a link between the dimerization modes and the autocleavage mechanism. We show that for the CTP1L endolysin, there is a reduction in lysis efficiency that is proportional to the cleavage efficiency. We propose a model for endolysin triggering, where the extended dimer presents the inactive state, and a switch to the side-by-side dimer triggers the cleavage of the C-terminal domain. This leads to the release of the catalytic portion of the endolysin, enabling the efficient digestion of the bacterial cell wall. Clostridium difficile infection is a common cause of hospital-acquired diarrhea, following broad-spectrum antibiotic treatment particularly in elderly patients. Bacteriophage therapy could provide an alternative treatment, but a better understanding of the viral components that lyse the bacterial cell is necessary. Here, we report on the activation of two endolysins from bacteriophages that lyse Clostridia. The structures of autoproteolytic fragments of two endolysins were determined by X-ray crystallography. Based on the structures, we introduced mutations that affect the autolytic cleavage of the enzymatic portion of the endolysins, and we show that two oligomeric states have an effect on the cleavage mechanism. Moreover, the lysis activity is affected when autocleavage is inhibited for one endolysin. We propose that the cleavage and oligomerization are linked, and they provide the endolysin with a trigger and release mechanism that leads to activation. The identification of a trigger and release factor may not only be relevant to Clostridia endolysins, but could be an important factor in the triggering of many bacteriophage endolysins. A fuller understanding of this activation mechanism will help in the design of recombinant endolysins or bacteriophages with a more efficient therapeutic potential.
Collapse
Affiliation(s)
- Matthew Dunne
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | | | | | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Andrew Thompson
- Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin, Gif sur Yvette, France
| | - Edward A. Lemke
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Melinda J. Mayer
- Institute of Food Research, Colney, Norwich, United Kingdom
- * E-mail: (MJM); (RM)
| | - Arjan Narbad
- Institute of Food Research, Colney, Norwich, United Kingdom
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
- * E-mail: (MJM); (RM)
| |
Collapse
|
61
|
|
62
|
Tamai E, Yoshida H, Sekiya H, Nariya H, Miyata S, Okabe A, Kuwahara T, Maki J, Kamitori S. X-ray structure of a novel endolysin encoded by episomal phage phiSM101 ofClostridium perfringens. Mol Microbiol 2014; 92:326-37. [DOI: 10.1111/mmi.12559] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Eiji Tamai
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Hiromi Yoshida
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Hirofumi Nariya
- Department of Microbiology; Faculty of Medicine; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Shigeru Miyata
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
- College of Bioscience and Biotechnology; Chubu University; 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
| | - Akinobu Okabe
- Department of Human Nutrition; Faculty of Contemporary Life Science; Chugokugakuen University; Niwase 83 Kita-ku Okayama 761-0197 Japan
| | - Tomomi Kuwahara
- Department of Microbiology; Faculty of Medicine; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Jun Maki
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Shigehiro Kamitori
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| |
Collapse
|
63
|
Crystal structures of CbpF complexed with atropine and ipratropium reveal clues for the design of novel antimicrobials against Streptococcus pneumoniae. Biochim Biophys Acta Gen Subj 2014; 1840:129-35. [DOI: 10.1016/j.bbagen.2013.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 11/16/2022]
|
64
|
Niu S, Luo M, Tang J, Zhou H, Zhang Y, Min X, Cai X, Zhang W, Xu W, Li D, Ding J, Hu Y, Wang D, Huang A, Yin Y, Wang D. Structural basis of the novel S. pneumoniae virulence factor, GHIP, a glycosyl hydrolase 25 participating in host-cell invasion. PLoS One 2013; 8:e68647. [PMID: 23874703 PMCID: PMC3712932 DOI: 10.1371/journal.pone.0068647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/30/2013] [Indexed: 11/20/2022] Open
Abstract
Pathogenic bacteria produce a wide variety of virulence factors that are considered to be potential antibiotic targets. In this study, we report the crystal structure of a novel S. pneumoniae virulence factor, GHIP, which is a streptococcus-specific glycosyl hydrolase. This novel structure exhibits an α/β-barrel fold that slightly differs from other characterized hydrolases. The GHIP active site, located at the negatively charged groove in the barrel, is very similar to the active site in known peptidoglycan hydrolases. Functionally, GHIP exhibited weak enzymatic activity to hydrolyze the PNP-(GlcNAc)5 peptidoglycan by the general acid/base catalytic mechanism. Animal experiments demonstrated a marked attenuation of S. pneumoniae-mediated virulence in mice infected by ΔGHIP-deficient strains, suggesting that GHIP functions as a novel S. pneumoniae virulence factor. Furthermore, GHIP participates in allowing S. pneumoniae to colonize the nasopharynx and invade host epithelial cells. Taken together, these findings suggest that GHIP can potentially serve as an antibiotic target to effectively treat streptococcus-mediated infection.
Collapse
Affiliation(s)
- Siqiang Niu
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
- The First Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Miao Luo
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Jian Tang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Hua Zhou
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yangli Zhang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Xun Min
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Xuefei Cai
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Wenlu Zhang
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Wenchu Xu
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Defeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Jingjin Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yonglin Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Dacheng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ailong Huang
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yibin Yin
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Deqiang Wang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, Chongqing, People’s Republic of China
| |
Collapse
|
65
|
Novel bacteriophage lysin with broad lytic activity protects against mixed infection by Streptococcus pyogenes and methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2013; 57:2743-50. [PMID: 23571534 DOI: 10.1128/aac.02526-12] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pyogenes (group A streptococcus [GrAS]) cause serious and sometimes fatal human diseases. They are among the many Gram-positive pathogens for which resistance to leading antibiotics has emerged. As a result, alternative therapies need to be developed to combat these pathogens. We have identified a novel bacteriophage lysin (PlySs2), derived from a Streptococcus suis phage, with broad lytic activity against MRSA, vancomycin-intermediate S. aureus (VISA), Streptococcus suis, Listeria, Staphylococcus simulans, Staphylococcus epidermidis, Streptococcus equi, Streptococcus agalactiae (group B streptococcus [GBS]), S. pyogenes, Streptococcus sanguinis, group G streptococci (GGS), group E streptococci (GES), and Streptococcus pneumoniae. PlySs2 has an N-terminal cysteine-histidine aminopeptidase (CHAP) catalytic domain and a C-terminal SH3b binding domain. It is stable at 50 °C for 30 min, 37 °C for >24 h, 4°C for 15 days, and -80 °C for >7 months; it maintained full activity after 10 freeze-thaw cycles. PlySs2 at 128 μg/ml in vitro reduced MRSA and S. pyogenes growth by 5 logs and 3 logs within 1 h, respectively, and exhibited a MIC of 16 μg/ml for MRSA. A single, 2-mg dose of PlySs2 protected 92% (22/24) of the mice in a bacteremia model of mixed MRSA and S. pyogenes infection. Serially increasing exposure of MRSA and S. pyogenes to PlySs2 or mupirocin resulted in no observed resistance to PlySs2 and resistance to mupirocin. To date, no other lysin has shown such notable broad lytic activity, stability, and efficacy against multiple, leading, human bacterial pathogens; as such, PlySs2 has all the characteristics to be an effective therapeutic.
Collapse
|
66
|
Fujisawa I, Kitamura Y, Okamoto R, Murayama K, Kato R, Aoki K. Crystal structure of pyrogallol[4]arene complex with phosphocholine: A molecular recognition model for phosphocholine through cation–π interaction. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.01.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
67
|
Ganguly J, Low LY, Kamal N, Saile E, Forsberg LS, Gutierrez-Sanchez G, Hoffmaster AR, Liddington R, Quinn CP, Carlson RW, Kannenberg EL. The secondary cell wall polysaccharide of Bacillus anthracis provides the specific binding ligand for the C-terminal cell wall-binding domain of two phage endolysins, PlyL and PlyG. Glycobiology 2013; 23:820-32. [PMID: 23493680 DOI: 10.1093/glycob/cwt019] [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] [Indexed: 12/15/2022] Open
Abstract
Endolysins are bacteriophage enzymes that lyse their bacterial host for phage progeny release. They commonly contain an N-terminal catalytic domain that hydrolyzes bacterial peptidoglycan (PG) and a C-terminal cell wall-binding domain (CBD) that confers enzyme localization to the PG substrate. Two endolysins, phage lysin L (PlyL) and phage lysin G (PlyG), are specific for Bacillus anthracis. To date, the cell wall ligands for their C-terminal CBD have not been identified. We recently described structures for a number of secondary cell wall polysaccharides (SCWPs) from B. anthracis and B. cereus strains. They are covalently bound to the PG and are comprised of a -ManNAc-GlcNAc-HexNAc- backbone with various galactosyl or glucosyl substitutions. Surface plasmon resonance (SPR) showed that the endolysins PlyL and PlyG bind to the SCWP from B. anthracis (SCWPBa) with high affinity (i.e. in the μM range with dissociation constants ranging from 0.81 × 10(-6) to 7.51 × 10(-6) M). In addition, the PlyL and PlyG SCWPBa binding sites reside with their C-terminal domains. The dissociation constants for the interactions of these endolysins and their derived C-terminal domains with the SCWPBa were in the range reported for other protein-carbohydrate interactions. Our findings show that the SCWPBa is the ligand that confers PlyL and PlyG lysin binding and localization to the PG. PlyL and PlyG also bound the SCWP from B. cereus G9241 with comparable affinities to SCWPBa. No detectable binding was found to the SCWPs from B. cereus ATCC (American Type Culture Collection) 10987 and ATCC 14579, thus demonstrating specificity of lysin binding to SCWPs.
Collapse
Affiliation(s)
- Jhuma Ganguly
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
68
|
Schmelcher M, Donovan DM, Loessner MJ. Bacteriophage endolysins as novel antimicrobials. Future Microbiol 2013; 7:1147-71. [PMID: 23030422 DOI: 10.2217/fmb.12.97] [Citation(s) in RCA: 524] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endolysins are enzymes used by bacteriophages at the end of their replication cycle to degrade the peptidoglycan of the bacterial host from within, resulting in cell lysis and release of progeny virions. Due to the absence of an outer membrane in the Gram-positive bacterial cell wall, endolysins can access the peptidoglycan and destroy these organisms when applied externally, making them interesting antimicrobial candidates, particularly in light of increasing bacterial drug resistance. This article reviews the modular structure of these enzymes, in which cell wall binding and catalytic functions are separated, as well as their mechanism of action, lytic activity and potential as antimicrobials. It particularly focuses on molecular engineering as a means of optimizing endolysins for specific applications, highlights new developments that may render these proteins active against Gram-negative and intracellular pathogens and summarizes the most recent applications of endolysins in the fields of medicine, food safety, agriculture and biotechnology.
Collapse
Affiliation(s)
- Mathias Schmelcher
- Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | | | | |
Collapse
|
69
|
Abstract
It is probably a biological constant that viruses are found associated with all known life and that they play an essential role in the ecology and evolution of all lifeforms. Lytic viruses have now been discovered that infect organisms from each of the three domains of life. Recently, a new lysis system has been described for two archaeal viruses. This lysis system appears to be novel and distinct from previously described virus-encoded lysis systems. A comparison of lytic viruses from each of the three domains may provide insights concerning the evolution of viruses.
Collapse
|
70
|
Microbial modulation of host immunity with the small molecule phosphorylcholine. Infect Immun 2012; 81:392-401. [PMID: 23230294 DOI: 10.1128/iai.01168-12] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
All microorganisms dependent on persistence in a host for survival rely on either hiding from or modulating host responses to infection. The small molecule phosphorylcholine, or choline phosphate (ChoP), is used for both of these purposes by a wide array of bacterial and parasitic microbes. While the mechanisms underlying ChoP acquisition and expression are diverse, a unifying theme is the use of ChoP to reduce the immune response to infection, creating an advantage for ChoP-expressing microorganisms. In this minireview, we discuss several benefits of ChoP expression during infection as well as how the immune system fights back against ChoP-expressing pathogens.
Collapse
|
71
|
|
72
|
Identification and characterization of an autolysin gene, atlA, from Streptococcus criceti. J Microbiol 2012; 50:777-84. [PMID: 23124745 DOI: 10.1007/s12275-012-2187-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/29/2012] [Indexed: 10/27/2022]
Abstract
AtlA of Streptococcus mutans is a major autolysin and belongs to glycoside hydrolase family 25 with cellosyl of Streptomyces coelicolor. The autolysin gene (atlA) encoding AtlA was identified from S. criceti. AtlA of S. criceti comprises the signal sequence in the N-terminus, the putative cell-wall-binding domain in the middle, and the catalytic domain in the C-terminus. Homology modeling analysis of the catalytic domain of AtlA showed the resemblance of the spatial arrangement of five amino acids around the predicted catalytic cavity to that of cellosyl. Recombinant AtlA and its four point mutants, D655A, D747A, W831A, and D849A, were evaluated on zymogram of S. criceti cells. Lytic activity was destroyed in the mutants D655A and D747A and diminished in the mutants W831A and D849A. These results suggest that Asp655 and Asp747 residues are critical for lytic activity and Trp831 and Asp849 residues are also associated with enzymatic activity.
Collapse
|
73
|
Abstract
Peptidoglycan (PG) is the major structural component of the bacterial cell wall. Bacteria have autolytic PG hydrolases that allow the cell to grow and divide. A well-studied group of PG hydrolase enzymes are the bacteriophage endolysins. Endolysins are PG-degrading proteins that allow the phage to escape from the bacterial cell during the phage lytic cycle. The endolysins, when purified and exposed to PG externally, can cause "lysis from without." Numerous publications have described how this phenomenon can be used therapeutically as an effective antimicrobial against certain pathogens. Endolysins have a characteristic modular structure, often with multiple lytic and/or cell wall-binding domains (CBDs). They degrade the PG with glycosidase, amidase, endopeptidase, or lytic transglycosylase activities and have been shown to be synergistic with fellow PG hydrolases or a range of other antimicrobials. Due to the coevolution of phage and host, it is thought they are much less likely to invoke resistance. Endolysin engineering has opened a range of new applications for these proteins from food safety to environmental decontamination to more effective antimicrobials that are believed refractory to resistance development. To put phage endolysin work in a broader context, this chapter includes relevant studies of other well-characterized PG hydrolase antimicrobials.
Collapse
|
74
|
Bustamante N, Rico-Lastres P, García E, García P, Menéndez M. Thermal stability of Cpl-7 endolysin from the streptococcus pneumoniae bacteriophage Cp-7; cell wall-targeting of its CW_7 motifs. PLoS One 2012; 7:e46654. [PMID: 23056389 PMCID: PMC3466307 DOI: 10.1371/journal.pone.0046654] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/02/2012] [Indexed: 11/28/2022] Open
Abstract
Endolysins comprise a novel class of selective antibacterials refractory to develop resistances. The Cpl-7 endolysin, encoded by the Streptococcus pneumoniae bacteriophage Cp-7, consists of a catalytic module (CM) with muramidase activity and a cell wall-binding module (CWBM) made of three fully conserved CW_7 repeats essential for activity. Firstly identified in the Cpl-7 endolysin, CW_7 motifs are also present in a great variety of cell wall hydrolases encoded, among others, by human and live-stock pathogens. However, the nature of CW_7 receptors on the bacterial envelope remains unknown. In the present study, the structural stability of Cpl-7 and the target recognized by CW_7 repeats, relevant for exploitation of Cpl-7 as antimicrobial, have been analyzed, and transitions from the CM and the CWBM assigned, using circular dichroism and differential scanning calorimetry. Cpl-7 stability is maximum around 6.0-6.5, near the optimal pH for activity. Above pH 8.0 the CM becomes extremely unstable, probably due to deprotonation of the N-terminal amino-group, whereas the CWBM is rather insensitive to pH variation and its structural stabilization by GlcNAc-MurNAc-l-Ala-d-isoGln points to the cell wall muropeptide as the cell wall target recognized by the CW_7 repeats. Denaturation data also revealed that Cpl-7 is organized into two essentially independent folding units, which will facilitate the recombination of the CM and the CWBM with other catalytic domains and/or cell wall-binding motifs to yield new tailored chimeric lysins with higher bactericidal activities or new pathogen specificities.
Collapse
Affiliation(s)
- Noemí Bustamante
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Palma Rico-Lastres
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ernesto García
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Pedro García
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| |
Collapse
|
75
|
Wall teichoic acids restrict access of bacteriophage endolysin Ply118, Ply511, and PlyP40 cell wall binding domains to the Listeria monocytogenes peptidoglycan. J Bacteriol 2012; 194:6498-506. [PMID: 23002226 DOI: 10.1128/jb.00808-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The C-terminal cell wall binding domains (CBDs) of phage endolysins direct the enzymes to their binding ligands on the bacterial cell wall with high affinity and specificity. The Listeria monocytogenes Ply118, Ply511, and PlyP40 endolysins feature related CBDs which recognize the directly cross-linked peptidoglycan backbone structure of Listeria. However, decoration with fluorescently labeled CBDs primarily occurs at the poles and septal regions of the rod-shaped cells. To elucidate the potential role of secondary cell wall-associated carbohydrates such as the abundant wall teichoic acid (WTA) on this phenomenon, we investigated CBD binding using L. monocytogenes serovar 1/2 and 4 cells deficient in WTA. Mutants were obtained by deletion of two redundant tagO homologues, whose products catalyze synthesis of the WTA linkage unit. While inactivation of either tagO1 (EGDe lmo0959) or tagO2 (EGDe lmo2519) alone did not affect WTA content, removal of both alleles following conditional complementation yielded WTA-deficient Listeria cells. Substitution of tagO from an isopropyl-β-d-thiogalactopyranoside-inducible single-copy integration vector restored the original phenotype. Although WTA-deficient cells are viable, they featured severe growth inhibition and an unusual coccoid morphology. In contrast to CBDs from other Listeria phage endolysins which directly utilize WTA as binding ligand, the data presented here show that WTAs are not required for attachment of CBD118, CBD511, and CBDP40. Instead, lack of the cell wall polymers enables unrestricted spatial access of CBDs to the cell wall surface, indicating that the abundant WTA can negatively regulate sidewall localization of the cell wall binding domains.
Collapse
|
76
|
X-ray crystal structure of the streptococcal specific phage lysin PlyC. Proc Natl Acad Sci U S A 2012; 109:12752-7. [PMID: 22807482 DOI: 10.1073/pnas.1208424109] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages deploy lysins that degrade the bacterial cell wall and facilitate virus egress from the host. When applied exogenously, these enzymes destroy susceptible microbes and, accordingly, have potential as therapeutic agents. The most potent lysin identified to date is PlyC, an enzyme assembled from two components (PlyCA and PlyCB) that is specific for streptococcal species. Here the structure of the PlyC holoenzyme reveals that a single PlyCA moiety is tethered to a ring-shaped assembly of eight PlyCB molecules. Structure-guided mutagenesis reveals that the bacterial cell wall binding is achieved through a cleft on PlyCB. Unexpectedly, our structural data reveal that PlyCA contains a glycoside hydrolase domain in addition to the previously recognized cysteine, histidine-dependent amidohydrolases/peptidases catalytic domain. The presence of eight cell wall-binding domains together with two catalytic domains may explain the extraordinary potency of the PlyC holoenyzme toward target bacteria.
Collapse
|
77
|
Pérez-Dorado I, Galan-Bartual S, Hermoso JA. Pneumococcal surface proteins: when the whole is greater than the sum of its parts. Mol Oral Microbiol 2012; 27:221-45. [PMID: 22759309 DOI: 10.1111/j.2041-1014.2012.00655.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Surface-exposed proteins of pathogenic bacteria are considered as potential virulence factors through their direct contribution to host-pathogen interactions. Four families of surface proteins decorate the cell surface of the human pathogen Streptococcus pneumoniae. Besides lipoproteins and LPXTG proteins, also present in other gram-positive bacteria, the pneumococcus presents the choline-binding protein (CBP) family and the non-classical surface proteins (NCSPs). The CBPs present specific structural features that allow their anchorage to the cell envelope through non-covalent interaction with choline residues of lipoteichoic acid and teichoic acid. NCSP is an umbrella term for less characterized proteins displaying moonlighting functions on the pneumococcal surface that lack a leader peptide and membrane-anchor motif. Considering the unceasing evolution of microbial species under the selective pressure of antibiotic use, detailed understanding of the interaction between pathogen and the host cells is required for the development of novel therapeutic strategies to combat pneumococcal infections. This article reviews recent progress in the investigation of the three-dimensional structures of surface-exposed pneumococcal proteins. The modular nature of some of them produces a great versatility and sophistication of the virulence functions that, in most cases, cannot be deduced by the structural analysis of the isolated modules.
Collapse
Affiliation(s)
- I Pérez-Dorado
- Department of Crystallography and Structural Biology, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain
| | | | | |
Collapse
|
78
|
Fenton M, Ross P, McAuliffe O, O'Mahony J, Coffey A. Recombinant bacteriophage lysins as antibacterials. Bioeng Bugs 2011; 1:9-16. [PMID: 21327123 DOI: 10.4161/bbug.1.1.9818] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 08/14/2009] [Indexed: 01/01/2023] Open
Abstract
With the increasing worldwide prevalence of antibiotic resistant bacteria, bacteriophage endolysins (lysins) represent a very promising novel alternative class of antibacterial in the fight against infectious disease. Lysins are phage-encoded peptidoglycan hydrolases which, when applied exogenously (as purified recombinant proteins) to Gram-positive bacteria, bring about rapid lysis and death of the bacterial cell. A number of studies have recently demonstrated the strong potential of these enzymes in human and veterinary medicine to control and treat pathogens on mucosal surfaces and in systemic infections. They also have potential in diagnostics and detection, bio-defence, elimination of food pathogens and control of phytopathogens. This review discusses the extensive research on recombinant bacteriophage lysins in the context of antibacterials, and looks forward to future development and potential.
Collapse
Affiliation(s)
- Mark Fenton
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | | | | | | | | |
Collapse
|
79
|
Fujisawa I, Takeuchi D, Kato R, Murayama K, Aoki K. Crystal Structures of Resorcin[4]arene and Tetramethylated Resorcin[4]arene Complexes Incorporating L-Carnitine through Cation–π Interaction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20110166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
80
|
Kajava AV. Tandem repeats in proteins: from sequence to structure. J Struct Biol 2011; 179:279-88. [PMID: 21884799 DOI: 10.1016/j.jsb.2011.08.009] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/15/2011] [Accepted: 08/17/2011] [Indexed: 10/17/2022]
Abstract
The bioinformatics analysis of proteins containing tandem repeats requires special computer programs and databases, since the conventional approaches predominantly developed for globular domains have limited success. Here, I survey bioinformatics tools which have been developed recently for identification and proteome-wide analysis of protein repeats. The last few years have also been marked by an emergence of new 3D structures of these proteins. Appraisal of the known structures and their classification uncovers a straightforward relationship between their architecture and the length of the repetitive units. This relationship and the repetitive character of structural folds suggest rules for better prediction of the 3D structures of such proteins. Furthermore, bioinformatics approaches combined with low resolution structural data, from biophysical techniques, especially, the recently emerged cryo-electron microscopy, lead to reliable prediction of the protein repeat structures and their mode of binding with partners within molecular complexes. This hybrid approach can actively be used for structural and functional annotations of proteomes.
Collapse
Affiliation(s)
- Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, Université Montpellier 1 et 2, 1919 Route de Mende, 34293 Montpellier, Cedex 5, France.
| |
Collapse
|
81
|
Low LY, Yang C, Perego M, Osterman A, Liddington R. Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins. J Biol Chem 2011; 286:34391-403. [PMID: 21816821 DOI: 10.1074/jbc.m111.244160] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The recombinant lysins of lytic phages, when applied externally to Gram-positive bacteria, can be efficient bactericidal agents, typically retaining high specificity. Their development as novel antibacterial agents offers many potential advantages over conventional antibiotics. Protein engineering could exploit this potential further by generating novel lysins fit for distinct target populations and environments. However, access to the peptidoglycan layer is controlled by a variety of secondary cell wall polymers, chemical modifications, and (in some cases) S-layers and capsules. Classical lysins require a cell wall-binding domain (CBD) that targets the catalytic domain to the peptidoglycan layer via binding to a secondary cell wall polymer component. The cell walls of Gram-positive bacteria generally have a negative charge, and we noticed a correlation between (positive) charge on the catalytic domain and bacteriolytic activity in the absence of the CBD (nonclassical behavior). We investigated a physical basis for this correlation by comparing the structures and activities of pairs of lysins where the lytic activity of one of each pair was CBD-independent. We found that by engineering a reversal of sign of the net charge of the catalytic domain, we could either eliminate or create CBD dependence. We also provide evidence that the S-layer of Bacillus anthracis acts as a molecular sieve that is chiefly size-dependent, favoring catalytic domains over full-length lysins. Our work suggests a number of facile approaches for fine-tuning lysin activity, either to enhance or reduce specificity/host range and/or bactericidal potential, as required.
Collapse
Affiliation(s)
- Lieh Yoon Low
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
| | | | | | | | | |
Collapse
|
82
|
Eugster MR, Haug MC, Huwiler SG, Loessner MJ. The cell wall binding domain of Listeria bacteriophage endolysin PlyP35 recognizes terminal GlcNAc residues in cell wall teichoic acid. Mol Microbiol 2011; 81:1419-32. [DOI: 10.1111/j.1365-2958.2011.07774.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
83
|
Structure-based modification of a Clostridium difficile-targeting endolysin affects activity and host range. J Bacteriol 2011; 193:5477-86. [PMID: 21803993 DOI: 10.1128/jb.00439-11] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Endolysin CD27L causes cell lysis of the pathogen Clostridium difficile, a major cause of nosocomial infection. We report a structural and functional analysis of the catalytic activity of CD27L against C. difficile and other bacterial strains. We show that truncation of the endolysin to the N-terminal domain, CD27L1-179, gave an increased lytic activity against cells of C. difficile, while the C-terminal region, CD27L180-270, failed to produce lysis. CD27L1-179 also has increased activity against other bacterial species that are targeted by the full-length protein and in addition was able to lyse some CD27L-insensitive strains. However, CD27L1-179 retained a measure of specificity, failing to lyse a wide range of bacteria. The use of green fluorescent protein (GFP)-labeled proteins demonstrated that both CD27L and CD27L1-179 bound to C. difficile cell walls. The crystal structure of CD27L1-179 confirms that the enzyme is a zinc-dependent N-acetylmuramoyl-l-alanine amidase. A structure-based sequence analysis allowed us to identify four catalytic residues, a proton relay cascade, and a substrate binding pocket. A BLAST search shows that the closest-related amidases almost exclusively target Clostridia. This implied that the catalytic domain alone contained features that target a specific bacterial species. To test this hypothesis, we modified Leu 98 to a Trp residue which is found in an endolysin from a bacteriophage of Listeria monocytogenes (PlyPSA). This mutation in CD27L resulted in an increased activity against selected serotypes of L. monocytogenes, demonstrating the potential to tune the species specificity of the catalytic domain of an endolysin.
Collapse
|
84
|
Schmelcher M, Tchang VS, Loessner MJ. Domain shuffling and module engineering of Listeria phage endolysins for enhanced lytic activity and binding affinity. Microb Biotechnol 2011; 4:651-62. [PMID: 21535426 PMCID: PMC3819014 DOI: 10.1111/j.1751-7915.2011.00263.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacteriophage endolysins are peptidoglycan hydrolases employed by the virus to lyse the host at the end of its multiplication phase. They have found many uses in biotechnology; not only as antimicrobials, but also for the development of novel diagnostic tools for rapid detection of pathogenic bacteria. These enzymes generally show a modular organization, consisting of N‐terminal enzymatically active domains (EADs) and C‐terminal cell wall‐binding domains (CBDs) which specifically target the enzymes to their substrate in the bacterial cell envelope. In this work, we used individual functional modules of Listeria phage endolysins to create fusion proteins with novel and optimized properties for labelling and lysis of Listeria cells. Chimaeras consisting of individual EAD and CBD modules from PlyPSA and Ply118 endolysins with different binding specificity and catalytic activity showed swapped properties. EAD118–CBDPSA fusion proteins exhibited up to threefold higher lytic activity than the parental endolysins. Recombineering different CBD domains targeting various Listeria cell surfaces into novel heterologous tandem proteins provided them with extended recognition and binding properties, as demonstrated by fluorescent GFP‐tagged CBD fusions. It was also possible to combine the binding specificities of different single CBDs in heterologous tandem CBD constructs such as CBD500‐P35 and CBDP35‐500, which were then able to recognize the majority of Listeria strains. Duplication of CBD500 increased the equilibrium cell wall binding affinity by approximately 50‐fold, and the enzyme featuring tandem CBD modules showed increased activity at higher ionic strength. Our results demonstrate that modular engineering of endolysins is a powerful approach for the rational design and optimization of desired functional properties of these proteins.
Collapse
Affiliation(s)
- Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zürich, Switzerland
| | | | | |
Collapse
|
85
|
Seal BS, Fouts DE, Simmons M, Garrish JK, Kuntz RL, Woolsey R, Schegg KM, Kropinski AM, Ackermann HW, Siragusa GR. Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions. Arch Virol 2011; 156:25-35. [PMID: 20963614 PMCID: PMC4127328 DOI: 10.1007/s00705-010-0812-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 08/27/2010] [Indexed: 10/18/2022]
Abstract
Poultry intestinal material, sewage and poultry processing drainage water were screened for virulent Clostridium perfringens bacteriophages. Viruses isolated from broiler chicken offal washes (O) and poultry feces (F), designated ΦCP39O and ΦCP26F, respectively, produced clear plaques on host strains. Both bacteriophages had isometric heads of 57 nm in diameter with 100-nm non-contractile tails characteristic of members of the family Siphoviridae in the order Caudovirales. The double-strand DNA genome of bacteriophage ΦCP39O was 38,753 base pairs (bp), while the ΦCP26F genome was 39,188 bp, with an average GC content of 30.3%. Both viral genomes contained 62 potential open reading frames (ORFs) predicted to be encoded on one strand. Among the ORFs, 29 predicted proteins had no known similarity while others encoded putative bacteriophage capsid components such as a pre-neck/appendage, tail, tape measure and portal proteins. Other genes encoded a predicted DNA primase, single-strand DNA-binding protein, terminase, thymidylate synthase and a transcription factor. Potential lytic enzymes such as a fibronectin-binding autolysin, an amidase/hydrolase and a holin were encoded in the viral genomes. Several ORFs encoded proteins that gave BLASTP matches with proteins from Clostridium spp. and other Gram-positive bacterial and bacteriophage genomes as well as unknown putative Collinsella aerofaciens proteins. Proteomics analysis of the purified viruses resulted in the identification of the putative pre-neck/appendage protein and a minor structural protein encoded by large open reading frames. Variants of the portal protein were identified, and several mycobacteriophage gp6-like protein variants were detected in large amounts relative to other virion proteins. The predicted amino acid sequences of the pre-neck/appendage proteins had major differences in the central portion of the protein between the two phage gene products. Based on phylogenetic analysis of the large terminase protein, these phages are predicted to be pac-type, using a head-full DNA packaging strategy.
Collapse
Affiliation(s)
- Bruce S Seal
- Richard B. Russell Agricultural Research Center, USDA, Athens, GA 30605, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
86
|
Lytic enzyme discovery through multigenomic sequence analysis in Clostridium perfringens. Appl Microbiol Biotechnol 2010; 89:1783-95. [PMID: 21085950 DOI: 10.1007/s00253-010-2982-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 10/23/2010] [Accepted: 10/25/2010] [Indexed: 10/18/2022]
Abstract
With their ability to lyse Gram-positive bacteria, phage lytic enzymes (or lysins) have received a great deal of attention as novel anti-infective agents. The number of known genes encoding these peptidoglycan hydrolases has increased markedly in recent years, due in large part to advances in DNA sequencing technology. As the genomes of more and more bacterial species/strains are sequenced, lysin-encoding open reading frames (ORFs) can be readily identified in lysogenized prophage regions. In the current study, we sought to assess lysin diversity for the medically relevant pathogen Clostridium perfringens. The sequenced genomes of nine C. perfringens strains were computationally mined for prophage lysins and lysin-like ORFs, revealing several dozen proteins of various enzymatic classes. Of these lysins, a muramidase from strain ATCC 13124 (termed PlyCM) was chosen for recombinant analysis based on its dissimilarity to previously characterized C. perfringens lysins. Following expression and purification, various biochemical properties of PlyCM were determined in vitro, including pH/salt-dependence and temperature stability. The enzyme exhibited activity at low μg/ml concentrations, a typical value for phage lysins. It was active against 23 of 24 strains of C. perfringens tested, with virtually no activity against other clostridial or non-clostridial species. Overall, PlyCM shows potential for development as an enzybiotic agent, demonstrating how expanding genomic databases can serve as rich pools for biotechnologically relevant proteins.
Collapse
|
87
|
Maestro B, Santiveri CM, Jiménez MA, Sanz JM. Structural autonomy of a β-hairpin peptide derived from the pneumococcal choline-binding protein LytA. Protein Eng Des Sel 2010; 24:113-22. [DOI: 10.1093/protein/gzq087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
88
|
Korczynska JE, Danielsen S, Schagerlöf U, Turkenburg JP, Davies GJ, Wilson KS, Taylor EJ. The structure of a family GH25 lysozyme from Aspergillus fumigatus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:973-7. [PMID: 20823508 PMCID: PMC2935209 DOI: 10.1107/s1744309110025601] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 06/29/2010] [Indexed: 11/11/2022]
Abstract
Lysins are important biomolecules which cleave the bacterial cell-wall polymer peptidoglycan. They are finding increasing commercial and medical application. In order to gain an insight into the mechanism by which these enzymes operate, the X-ray structure of a CAZy family GH25 ;lysozyme' from Aspergillus fumigatus was determined. This is the first fungal structure from the family and reveals a modified alpha/beta-barrel-like fold in which an eight-stranded beta-barrel is flanked by three alpha-helices. The active site lies toward the bottom of a negatively charged pocket and its layout has much in common with other solved members of the GH25 and related GH families. A conserved active-site DXE motif may be implicated in catalysis, lending further weight to the argument that this glycoside hydrolase family operates via a ;substrate-assisted' catalytic mechanism.
Collapse
Affiliation(s)
- Justyna E. Korczynska
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England
| | | | | | - Johan P. Turkenburg
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England
| | - Gideon J. Davies
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England
| | - Keith S. Wilson
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England
| | - Edward J. Taylor
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England
| |
Collapse
|
89
|
Genome sequence of the temperate bacteriophage PH10 from Streptococcus oralis. Virus Genes 2010; 41:450-8. [PMID: 20803062 DOI: 10.1007/s11262-010-0525-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 08/17/2010] [Indexed: 10/19/2022]
Abstract
Exponential growing cultures of Streptococcus oralis strain OMZ 1038, isolated from human supragingival dental plaque, were found to release a bacteriophage (designated PH10) upon treatment with mitomycin C. The complete genome sequence of phage PH10 was determined. The genome was 31276 bp in size and contained 54 open reading frames. The module encoding structural proteins was highly similar to that of Streptococcus pneumoniae prophage PhiSpn_3. The most abundant phage structural protein was encoded by ORF35 and was likely processed by proteolytic cleavage. The putative endolysin from PH10, which contained a muramidase domain and a choline-binding domain, was purified and shown to have lytic activity with S. oralis, S. pneumoniae and Streptococcus mitis, but not with other streptococcal species.
Collapse
|
90
|
Bustamante N, Campillo NE, García E, Gallego C, Pera B, Diakun GP, Sáiz JL, García P, Díaz JF, Menéndez M. Cpl-7, a lysozyme encoded by a pneumococcal bacteriophage with a novel cell wall-binding motif. J Biol Chem 2010; 285:33184-33196. [PMID: 20720016 DOI: 10.1074/jbc.m110.154559] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage endolysins include a group of new antibacterials reluctant to development of resistance. We present here the first structural study of the Cpl-7 endolysin, encoded by pneumococcal bacteriophage Cp-7. It contains an N-terminal catalytic module (CM) belonging to the GH25 family of glycosyl hydrolases and a C-terminal region encompassing three identical repeats of 42 amino acids (CW_7 repeats). These repeats are unrelated to choline-targeting motifs present in other cell wall hydrolases produced by Streptococcus pneumoniae and its bacteriophages, and are responsible for the protein attachment to the cell wall. By combining different biophysical techniques and molecular modeling, a three-dimensional model of the overall protein structure is proposed, consistent with circular dichroism and sequence-based secondary structure prediction, small angle x-ray scattering data, and Cpl-7 hydrodynamic behavior. Cpl-7 is an ∼115-Å long molecule with two well differentiated regions, corresponding to the CM and the cell wall binding region (CWBR), arranged in a lateral disposition. The CM displays the (βα)(5)β(3) barrel topology characteristic of the GH25 family, and the impact of sequence differences with the CM of the Cpl-1 lysozyme in substrate binding is discussed. The CWBR is organized in three tandemly assembled three-helical bundles whose dispositions remind us of a super-helical structure. Its approximate dimensions are 60 × 20 × 20 Å and presents a concave face that might constitute the functional region involved in bacterial surface recognition. The distribution of CW_7 repeats in the sequences deposited in the Entrez Database have been examined, and the results drastically expanded the antimicrobial potential of the Cpl-7 endolysin.
Collapse
Affiliation(s)
- Noemí Bustamante
- From the Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; CIBER de Enfermedades Respiratorias, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Nuria E Campillo
- Instituto de Química Médica, Consejo Superior de Investigaciones Científicas, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Ernesto García
- CIBER de Enfermedades Respiratorias, Juan de la Cierva 3, 28006 Madrid, Spain; Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Cristina Gallego
- From the Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; CIBER de Enfermedades Respiratorias, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Benet Pera
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - José Luis Sáiz
- From the Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; CIBER de Enfermedades Respiratorias, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Pedro García
- CIBER de Enfermedades Respiratorias, Juan de la Cierva 3, 28006 Madrid, Spain; Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - J Fernando Díaz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Margarita Menéndez
- From the Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; CIBER de Enfermedades Respiratorias, Juan de la Cierva 3, 28006 Madrid, Spain.
| |
Collapse
|
91
|
Silva-Martin N, Molina R, Angulo I, Mancheño JM, García P, Hermoso JA. Crystallization and preliminary crystallographic analysis of the catalytic module of endolysin from Cp-7, a phage infecting Streptococcus pneumoniae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:670-3. [PMID: 20516596 PMCID: PMC2882766 DOI: 10.1107/s1744309110006718] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 02/22/2010] [Indexed: 11/10/2022]
Abstract
As part of the life cycle of the pneumococcal phage Cp-7, the endolysin Cpl-7 cleaves the glycosidic beta1,4 bonds between N-acetylmuramic acid and N-acetylglucosamine in the pneumococcal cell wall, resulting in bacterial lysis. Recombinant Cpl-7 was overexpressed in Escherichia coli, purified and crystallized using the vapour-diffusion method at 291 K. Diffraction-quality tetragonal crystals of the catalytic module of Cpl-7 were obtained from a mixture of PEG 3350 and sodium formate. The crystals belonged to space group I422, with unit-cell parameters a = 127.93, b = 127.93, c = 82.07 A. Diffraction data sets were collected to 2.4 A resolution using a rotating-anode generator.
Collapse
Affiliation(s)
- Noella Silva-Martin
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Rafael Molina
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Ivan Angulo
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - José M. Mancheño
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Pedro García
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Juan A. Hermoso
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| |
Collapse
|
92
|
Bacteriophage endolysins: a novel anti-infective to control Gram-positive pathogens. Int J Med Microbiol 2010; 300:357-62. [PMID: 20452280 DOI: 10.1016/j.ijmm.2010.04.002] [Citation(s) in RCA: 296] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Endolysins (or lysins) are highly evolved enzymes produced by bacteriophage (phage for short) to digest the bacterial cell wall for phage progeny release. In Gram-positive bacteria, small quantities of purified recombinant lysin added externally results in immediate lysis causing log-fold death of the target bacterium. Lysins have been used successfully in a variety of animal models to control pathogenic antibiotic-resistant bacteria found on mucosal surfaces and infected tissues. Their specificity for the pathogen without disturbing the normal flora, the low chance of bacterial resistance, and their ability to kill colonizing pathogens on mucosal surfaces, a capacity previously unavailable, make them ideal anti-infectives in an age of mounting resistance. Here we review the current literature showing the effectiveness of these enzymes in controlling a variety of infections.
Collapse
|
93
|
Pérez-Dorado I, González A, Morales M, Sanles R, Striker W, Vollmer W, Mobashery S, García JL, Martínez-Ripoll M, García P, Hermoso JA. Insights into pneumococcal fratricide from the crystal structures of the modular killing factor LytC. Nat Struct Mol Biol 2010; 17:576-81. [PMID: 20400948 DOI: 10.1038/nsmb.1817] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 02/23/2010] [Indexed: 11/09/2022]
Abstract
The first structure of a pneumococcal autolysin, that of the LytC lysozyme, has been solved in ternary complex with choline and a pneumococcal peptidoglycan (PG) fragment. The active site of the hydrolase module is not fully exposed but is oriented toward the choline-binding module, which accounts for its unique in vivo features in PG hydrolysis, its activation and its regulatory mechanisms. Because of the unusual hook-shaped conformation of the multimodular protein, it is only able to hydrolyze non-cross-linked PG chains, an assertion validated by additional experiments. These results explain the activation of LytC by choline-binding protein D (CbpD) in fratricide, a competence-programmed mechanism of predation of noncompetent sister cells. The results provide the first structural insights to our knowledge into the critical and central function that LytC plays in pneumococcal virulence and explain a long-standing puzzle of how murein hydrolases can be controlled to avoid self-lysis during bacterial growth and division.
Collapse
Affiliation(s)
- Inmaculada Pérez-Dorado
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
94
|
Zhang Z, Li W, Frolet C, Bao R, di Guilmi AM, Vernet T, Chen Y. Structure of the choline-binding domain of Spr1274 in Streptococcus pneumoniae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:757-61. [PMID: 19652332 PMCID: PMC2720326 DOI: 10.1107/s1744309109025329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 06/30/2009] [Indexed: 11/10/2022]
Abstract
Spr1274 is a putative choline-binding protein that is bound to the cell wall of Streptococcus pneumoniae through noncovalent interactions with the choline moieties of teichoic and lipoteichoic acids. Its function is still unknown. The crystal structure of the choline-binding domain of Spr1274 (residues 44-129) was solved at 2.38 A resolution with three molecules in the asymmetric unit. It may provide a structural basis for functional analysis of choline-binding proteins.
Collapse
Affiliation(s)
- Zhenyi Zhang
- Protein Research Institute, Tongji University, Shanghai 200092, People’s Republic of China
| | - Wenzhe Li
- Protein Research Institute, Tongji University, Shanghai 200092, People’s Republic of China
| | - Cecile Frolet
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Laboratoire d’Ingénierie des Macromolécules, 41 Rue Jules Horowitz, and CEA, Université Joseph Fourier, Partnership for Structural Biology, 38027 Grenoble, France
| | - Rui Bao
- Protein Research Institute, Tongji University, Shanghai 200092, People’s Republic of China
| | - Anne-Marie di Guilmi
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Laboratoire d’Ingénierie des Macromolécules, 41 Rue Jules Horowitz, and CEA, Université Joseph Fourier, Partnership for Structural Biology, 38027 Grenoble, France
| | - Thierry Vernet
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Laboratoire d’Ingénierie des Macromolécules, 41 Rue Jules Horowitz, and CEA, Université Joseph Fourier, Partnership for Structural Biology, 38027 Grenoble, France
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| |
Collapse
|
95
|
Cloning, expression, and characterization of a peculiar choline-binding beta-galactosidase from Streptococcus mitis. Appl Environ Microbiol 2009; 75:5972-80. [PMID: 19633119 DOI: 10.1128/aem.00618-09] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Streptococcus mitis genomic DNA fragment carrying the SMT1224 gene encoding a putative beta-galactosidase was identified, cloned, and expressed in Escherichia coli. This gene encodes a protein 2,411 amino acids long with a predicted molecular mass of 268 kDa. The deduced protein contains an N-terminal signal peptide and a C-terminal choline-binding domain consisting of five consensus repeats, which facilitates the anchoring of the secreted enzyme to the cell wall. The choline-binding capacity of the protein facilitates its purification using DEAE-cellulose affinity chromatography, although its complete purification was achieved by constructing a His-tagged fusion protein. The recombinant protein was characterized as a monomeric beta-galactosidase showing a specific activity of around 2,500 U/mg of protein, with optimum temperature and pH ranges of 30 to 40 degrees C and 6.0 to 6.5, respectively. Enzyme activity is not inhibited by glucose, even at 200 mM, and remains highly stable in solution or immobilized at room temperature in the absence of protein stabilizers. In S. mitis, the enzyme was located attached to the cell surface, but a significant activity was also detected in the culture medium. This novel enzyme represents the first beta-galactosidase having a modular structure with a choline-binding domain, a peculiar property that can also be useful for some biotechnological applications.
Collapse
|
96
|
Martinez-Fleites C, Korczynska JE, Davies GJ, Cope MJ, Turkenburg JP, Taylor EJ. The crystal structure of a family GH25 lysozyme from Bacillus anthracis implies a neighboring-group catalytic mechanism with retention of anomeric configuration. Carbohydr Res 2009; 344:1753-7. [PMID: 19595298 DOI: 10.1016/j.carres.2009.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 05/27/2009] [Accepted: 06/01/2009] [Indexed: 11/30/2022]
Abstract
Lysozymes are found in many of the sequence-based families of glycoside hydrolases (www.cazy.org) where they show considerable structural and mechanistic diversity. Lysozymes from glycoside hydrolase family GH25 adopt a (alpha/beta)(5)(beta)(3)-barrel-like fold with a proposal in the literature that these enzymes act with inversion of anomeric configuration; the lack of a suitable substrate, however, means that no group has successfully demonstrated the configuration of the product. Here we report the 3-D structure of the GH25 enzyme from Bacillus anthracis at 1.4A resolution. We show that the active center is extremely similar to those from glycoside hydrolase families GH18, GH20, GH56, GH84, and GH85 implying that, in the absence of evidence to the contrary, GH25 enzymes also act with net retention of anomeric configuration using the neighboring-group catalytic mechanism that is common to this 'super-family' of enzymes.
Collapse
Affiliation(s)
- Carlos Martinez-Fleites
- Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5YW, United Kingdom
| | | | | | | | | | | |
Collapse
|
97
|
Vocadlo DJ, Davies GJ. Mechanistic insights into glycosidase chemistry. Curr Opin Chem Biol 2009; 12:539-55. [PMID: 18558099 DOI: 10.1016/j.cbpa.2008.05.010] [Citation(s) in RCA: 312] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/16/2022]
Abstract
The enzymatic hydrolysis of the glycosidic bond continues to gain importance, reflecting the critically important roles complex glycans play in health and disease as well as the rekindled interest in enzymatic biomass conversion. Recent advances include the broadening of our understanding of enzyme reaction coordinates, through both computational and structural studies, improved understanding of enzyme inhibition through transition state mimicry and fascinating insights into mechanism yielded by physical organic chemistry approaches.
Collapse
Affiliation(s)
- David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, Canada.
| | | |
Collapse
|
98
|
Crystal structure of CbpF, a bifunctional choline-binding protein and autolysis regulator from Streptococcus pneumoniae. EMBO Rep 2009; 10:246-51. [PMID: 19165143 DOI: 10.1038/embor.2008.245] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 12/02/2008] [Accepted: 12/04/2008] [Indexed: 11/08/2022] Open
Abstract
Phosphorylcholine, a crucial component of the pneumococcal cell wall, is essential in bacterial physiology and in human pathogenesis because it binds to serum components of the immune system and acts as a docking station for the family of surface choline-binding proteins. The three-dimensional structure of choline-binding protein F (CbpF), one of the most abundant proteins in the pneumococcal cell wall, has been solved in complex with choline. CbpF shows a new modular structure composed both of consensus and non-consensus choline-binding repeats, distributed along its length, which markedly alter its shape, charge distribution and binding ability, and organizing the protein into two well-defined modules. The carboxy-terminal module is involved in cell wall binding and the amino-terminal module is crucial for inhibition of the autolytic LytC muramidase, providing a regulatory function for pneumococcal autolysis.
Collapse
|
99
|
Hernández-Rocamora V, Maestro B, de Waal B, Morales M, García P, Meijer E, Merkx M, Sanz J. Multivalent Choline Dendrimers as Potent Inhibitors of Pneumococcal Cell-Wall Hydrolysis. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200803664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
100
|
Hernández-Rocamora V, Maestro B, de Waal B, Morales M, García P, Meijer E, Merkx M, Sanz J. Multivalent Choline Dendrimers as Potent Inhibitors of Pneumococcal Cell-Wall Hydrolysis. Angew Chem Int Ed Engl 2009; 48:948-51. [DOI: 10.1002/anie.200803664] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|