1
|
Blondel CJ, Amaya FA, Bustamante P, Santiviago CA, Pezoa D. Identification and distribution of new candidate T6SS effectors encoded in Salmonella Pathogenicity Island 6. Front Microbiol 2023; 14:1252344. [PMID: 37664116 PMCID: PMC10469887 DOI: 10.3389/fmicb.2023.1252344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
The type VI secretion system (T6SS) is a contact-dependent contractile multiprotein apparatus widely distributed in Gram-negative bacteria. These systems can deliver different effector proteins into target bacterial and/or eukaryotic cells, contributing to the environmental fitness and virulence of many bacterial pathogens. Salmonella harbors five different T6SSs encoded in different genomic islands. The T6SS encoded in Salmonella Pathogenicity Island 6 (SPI-6) contributes to Salmonella competition with the host microbiota and its interaction with infected host cells. Despite its relevance, information regarding the total number of effector proteins encoded within SPI-6 and its distribution among different Salmonella enterica serotypes is limited. In this work, we performed bioinformatic and comparative genomics analyses of the SPI-6 T6SS gene cluster to expand our knowledge regarding the T6SS effector repertoire and the global distribution of these effectors in Salmonella. The analysis of a curated dataset of 60 Salmonella enterica genomes from the Secret6 database revealed the presence of 23 new putative T6SS effector/immunity protein (E/I) modules. These effectors were concentrated in the variable regions 1 to 3 (VR1-3) of the SPI-6 T6SS gene cluster. VR1-2 were enriched in candidate effectors with predicted peptidoglycan hydrolase activity, while VR3 was enriched in candidate effectors of the Rhs family with C-terminal extensions with predicted DNase, RNase, deaminase, or ADP-ribosyltransferase activity. A global analysis of known and candidate effector proteins in Salmonella enterica genomes from the NCBI database revealed that T6SS effector proteins are differentially distributed among Salmonella serotypes. While some effectors are present in over 200 serotypes, others are found in less than a dozen. A hierarchical clustering analysis identified Salmonella serotypes with distinct profiles of T6SS effectors and candidate effectors, highlighting the diversity of T6SS effector repertoires in Salmonella enterica. The existence of different repertoires of effector proteins suggests that different effector protein combinations may have a differential impact on the environmental fitness and pathogenic potential of these strains.
Collapse
Affiliation(s)
- Carlos J. Blondel
- Facultad de Medicina y Facultad de Ciencias de la Vida, Instituto de Ciencias Biomédicas, Universidad Andrés Bello, Santiago, Chile
| | - Fernando A. Amaya
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Paloma Bustamante
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Carlos A. Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - David Pezoa
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
- Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O'Higgins, Santiago, Chile
| |
Collapse
|
2
|
Griffin ME, Klupt S, Espinosa J, Hang HC. Peptidoglycan NlpC/P60 peptidases in bacterial physiology and host interactions. Cell Chem Biol 2023; 30:436-456. [PMID: 36417916 PMCID: PMC10192474 DOI: 10.1016/j.chembiol.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall is composed of a highly crosslinked matrix of glycopeptide polymers known as peptidoglycan that dictates bacterial cell morphology and protects against environmental stresses. Regulation of peptidoglycan turnover is therefore crucial for bacterial survival and growth and is mediated by key protein complexes and enzyme families. Here, we review the prevalence, structure, and activity of NlpC/P60 peptidases, a family of peptidoglycan hydrolases that are crucial for cell wall turnover and division as well as interactions with antibiotics and different hosts. Understanding the molecular functions of NlpC/P60 peptidases should provide important insight into bacterial physiology, their interactions with different kingdoms of life, and the development of new therapeutic approaches.
Collapse
Affiliation(s)
- Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Steven Klupt
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.
| |
Collapse
|
3
|
Tandukar S, Kwon E, Kim DY. Structural insights into the regulation of peptidoglycan DL-endopeptidases by inhibitory protein IseA. Structure 2023; 31:619-628.e4. [PMID: 36963396 DOI: 10.1016/j.str.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/29/2023] [Accepted: 02/27/2023] [Indexed: 03/26/2023]
Abstract
Peptidoglycan, a physical barrier that protects bacteria from the environment, is constantly degraded and resynthesized for remodeling during cell growth and division. Because excessive or insufficient peptidoglycan hydrolysis affects bacterial homeostasis and viability, peptidoglycan degradation must be precisely regulated. In Bacillus subtilis, DL-endopeptidases play an essential role in peptidoglycan remodeling, and their activity is regulated by IseA. Here, we report the crystal structure of peptidoglycan DL-endopeptidase LytE complexed with IseA. In the crystal structure, the inhibitory loop connecting the two lobes of IseA blocks the active site of LytE by mimicking its substrate. Consistently, mutations in the inhibitory loop resulted in the loss of IseA activity. The structure also shows that conformational rearrangements in both LytE and IseA restrict access of the inhibitory loop to the LytE catalytic site. These results reveal an inhibition mechanism of peptidoglycan DL-endopeptidase in which the inhibitory protein mimics the substrate but is not degraded.
Collapse
Affiliation(s)
| | - Eunju Kwon
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, South Korea.
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, South Korea.
| |
Collapse
|
4
|
Reuter J, Otten C, Jacquier N, Lee J, Mengin-Lecreulx D, Löckener I, Kluj R, Mayer C, Corona F, Dannenberg J, Aeby S, Bühl H, Greub G, Vollmer W, Ouellette SP, Schneider T, Henrichfreise B. An NlpC/P60 protein catalyzes a key step in peptidoglycan recycling at the intersection of energy recovery, cell division and immune evasion in the intracellular pathogen Chlamydia trachomatis. PLoS Pathog 2023; 19:e1011047. [PMID: 36730465 PMCID: PMC9928106 DOI: 10.1371/journal.ppat.1011047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/14/2023] [Accepted: 12/06/2022] [Indexed: 02/04/2023] Open
Abstract
The obligate intracellular Chlamydiaceae do not need to resist osmotic challenges and thus lost their cell wall in the course of evolution. Nevertheless, these pathogens maintain a rudimentary peptidoglycan machinery for cell division. They build a transient peptidoglycan ring, which is remodeled during the process of cell division and degraded afterwards. Uncontrolled degradation of peptidoglycan poses risks to the chlamydial cell, as essential building blocks might get lost or trigger host immune response upon release into the host cell. Here, we provide evidence that a primordial enzyme class prevents energy intensive de novo synthesis and uncontrolled release of immunogenic peptidoglycan subunits in Chlamydia trachomatis. Our data indicate that the homolog of a Bacillus NlpC/P60 protein is widely conserved among Chlamydiales. We show that the enzyme is tailored to hydrolyze peptidoglycan-derived peptides, does not interfere with peptidoglycan precursor biosynthesis, and is targeted by cysteine protease inhibitors in vitro and in cell culture. The peptidase plays a key role in the underexplored process of chlamydial peptidoglycan recycling. Our study suggests that chlamydiae orchestrate a closed-loop system of peptidoglycan ring biosynthesis, remodeling, and recycling to support cell division and maintain long-term residence inside the host. Operating at the intersection of energy recovery, cell division and immune evasion, the peptidoglycan recycling NlpC/P60 peptidase could be a promising target for the development of drugs that combine features of classical antibiotics and anti-virulence drugs.
Collapse
Affiliation(s)
- Jula Reuter
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Christian Otten
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Nicolas Jacquier
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Junghoon Lee
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Dominique Mengin-Lecreulx
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Iris Löckener
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Robert Kluj
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Federico Corona
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Julia Dannenberg
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Sébastien Aeby
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Henrike Bühl
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Scot P. Ouellette
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Beate Henrichfreise
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| |
Collapse
|
5
|
Biochemical Characterizations of the Putative Endolysin Ecd09610 Catalytic Domain from Clostridioides difficile. Antibiotics (Basel) 2022; 11:antibiotics11081131. [PMID: 36010000 PMCID: PMC9405191 DOI: 10.3390/antibiotics11081131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Clostridioides difficile is the major pathogen of pseudomembranous colitis, and novel antimicrobial agents are sought after for its treatment. Phage-derived endolysins with species-specific lytic activity have potential as novel antimicrobial agents. We surveyed the genome of C. difficile strain 630 and identified an endolysin gene, Ecd09610, which has an uncharacterized domain at the N-terminus and two catalytic domains that are homologous to glucosaminidase and endopeptidase at the C-terminus. Genes containing the two catalytic domains, the glucosaminidase domain and the endopeptidase domain, were cloned and expressed in Escherichia coli as N-terminal histidine-tagged proteins. The purified domain variants showed lytic activity almost specifically for C. difficile, which has a unique peptide bridge in its peptidoglycan. This species specificity is thought to depend on substrate cleavage activity rather than binding. The domain variants were thermostable, and, notably, the glucosaminidase domain remained active up to 100 °C. In addition, we determined the optimal pH and salt concentrations of these domain variants. Their properties are suitable for formulating a bacteriolytic enzyme as an antimicrobial agent. This lytic enzyme can serve as a scaffold for the construction of high lytic activity mutants with enhanced properties.
Collapse
|
6
|
Nakonieczna A, Rutyna P, Fedorowicz M, Kwiatek M, Mizak L, Łobocka M. Three Novel Bacteriophages, J5a, F16Ba, and z1a, Specific for Bacillus anthracis, Define a New Clade of Historical Wbeta Phage Relatives. Viruses 2022; 14:v14020213. [PMID: 35215807 PMCID: PMC8878798 DOI: 10.3390/v14020213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus anthracis is a potent biowarfare agent, able to be highly lethal. The bacteria dwell in the soil of certain regions, as natural flora. Bacteriophages or their lytic enzymes, endolysins, may be an alternative for antibiotics and other antibacterials to fight this pathogen in infections and to minimize environmental contamination with anthrax endospores. Upon screening environmental samples from various regions in Poland, we isolated three new siphophages, J5a, F16Ba, and z1a, specific for B. anthracis. They represent new species related to historical anthrax phages Gamma, Cherry, and Fah, and to phage Wbeta of Wbetavirus genus. We show that the new phages and their closest relatives, phages Tavor_SA, Negev_SA, and Carmel_SA, form a separate clade of the Wbetavirus genus, designated as J5a clade. The most distinctive feature of J5a clade phages is their cell lysis module. While in the historical phages it encodes a canonical endolysin and a class III holin, in J5a clade phages it encodes an endolysin with a signal peptide and two putative holins. We present the basic characteristic of the isolated phages. Their comparative genomic analysis indicates that they encode two receptor-binding proteins, of which one may bind a sugar moiety of B. anthracis cell surface.
Collapse
Affiliation(s)
- Aleksandra Nakonieczna
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
- Correspondence: (A.N.); (M.Ł.)
| | - Paweł Rutyna
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Magdalena Fedorowicz
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Magdalena Kwiatek
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Lidia Mizak
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106 Warsaw, Poland
- Correspondence: (A.N.); (M.Ł.)
| |
Collapse
|
7
|
Structural Investigations on the SH3b Domains of Clostridium perfringens Autolysin through NMR Spectroscopy and Structure Simulation Enlighten the Cell Wall Binding Function. Molecules 2021; 26:molecules26185716. [PMID: 34577187 PMCID: PMC8470621 DOI: 10.3390/molecules26185716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Clostridium perfringens autolysin (CpAcp) is a peptidoglycan hydrolase associated with cell separation, division, and growth. It consists of a signal peptide, ten SH3b domains, and a catalytic domain. The structure and function mechanisms of the ten SH3bs related to cell wall peptidoglycan binding remain unclear. Here, the structures of CpAcp SH3bs were studied through NMR spectroscopy and structural simulation. The NMR structure of SH3b6 was determined at first, which adopts a typical β-barrel fold and has three potential ligand-binding pockets. The largest pocket containing eight conserved residues was suggested to bind with peptide ligand in a novel model. The structures of the other nine SH3bs were subsequently predicted to have a fold similar to SH3b6. Their ligand pockets are largely similar to those of SH3b6, although with varied size and morphology, except that SH3b1/2 display a third pocket markedly different from those in other SH3bs. Thus, it was supposed that SH3b3-10 possess similar ligand-binding ability, while SH3b1/2 have a different specificity and additional binding site for ligand. As an entirety, ten SH3bs confer a capacity for alternatively binding to various peptidoglycan sites in the cell wall. This study presents an initial insight into the structure and potential function of CpAcp SH3bs.
Collapse
|
8
|
Zouhir S, Contreras-Martel C, Maragno Trindade D, Attrée I, Dessen A, Macheboeuf P. MagC is a NplC/P60-like member of the α-2-macroglobulin Mag complex of Pseudomonas aeruginosa that interacts with peptidoglycan. FEBS Lett 2021; 595:2034-2046. [PMID: 34115884 DOI: 10.1002/1873-3468.14148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/17/2021] [Accepted: 06/08/2021] [Indexed: 11/07/2022]
Abstract
Bacterial α-2 macroglobulins (A2Ms) structurally resemble the large spectrum protease inhibitors of the eukaryotic immune system. In Pseudomonas aeruginosa, MagD acts as an A2M and is expressed within a six-gene operon encoding the MagA-F proteins. In this work, we employ isothermal calorimetry (ITC), analytical ultracentrifugation (AUC), and X-ray crystallography to investigate the function of MagC and show that MagC associates with the macroglobulin complex and with the peptidoglycan (PG). However, the catalytic residues of MagC display an inactive conformation that could suggest that it binds to PG but does not degrade it. We hypothesize that MagC could serve as an anchor between the MagD macroglobulin and the PG and could provide stabilization and/or regulation for the entire complex.
Collapse
Affiliation(s)
- Samira Zouhir
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, Brazil
| | | | | | - Ina Attrée
- Unité de Biologie Cellulaire et Infection, CEA, INSERM, CNRS, Université Grenoble Alpes, France
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, Brazil.,CNRS, CEA, IBS, Université Grenoble Alpes, France
| | | |
Collapse
|
9
|
Espinosa J, Lin TY, Estrella Y, Kim B, Molina H, Hang HC. Enterococcus NlpC/p60 Peptidoglycan Hydrolase SagA Localizes to Sites of Cell Division and Requires Only a Catalytic Dyad for Protease Activity. Biochemistry 2020; 59:4470-4480. [PMID: 33136372 DOI: 10.1021/acs.biochem.0c00755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptidoglycan is a vital component of the bacterial cell wall, and its dynamic remodeling by NlpC/p60 hydrolases is crucial for proper cell division and survival. Beyond these essential functions, we previously discovered that Enterococcus species express and secrete the NlpC/p60 hydrolase-secreted antigen A (SagA), whose catalytic activity can modulate host immune responses in animal models. However, the localization and peptidoglycan hydrolase activity of SagA in Enterococcus was still unclear. In this study, we show that SagA contributes to a triseptal structure in dividing cells of enterococci and localizes to sites of cell division through its N-terminal coiled-coil domain. Using molecular modeling and site-directed mutagenesis, we identify amino acid residues within the SagA-NlpC/p60 domain that are crucial for catalytic activity and potential substrate binding. Notably, these studies revealed that SagA may function via a catalytic Cys-His dyad instead of the predicted Cys-His-His triad, which is conserved in SagA orthologs from other Enterococcus species. Our results provide key additional insight into peptidoglycan remodeling in Enterococcus by SagA NlpC/p60 hydrolases.
Collapse
Affiliation(s)
- Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Ti-Yu Lin
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Yadyvic Estrella
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Byungchul Kim
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States.,Departments of Immunology & Microbiology and Chemistry, Scripps Research, La Jolla, California 92037, United States
| |
Collapse
|
10
|
Sekiya H, Tamai E, Kawasaki J, Murakami K, Kamitori S. Structural and biochemical characterizations of the novel autolysin Acd24020 from Clostridioides difficile and its full-function catalytic domain as a lytic enzyme. Mol Microbiol 2020; 115:684-698. [PMID: 33140473 DOI: 10.1111/mmi.14636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/13/2020] [Accepted: 10/28/2020] [Indexed: 12/17/2022]
Abstract
Autolysin is a lytic enzyme that hydrolyzes peptidoglycans of the bacterial cell wall, with a catalytic domain and cell wall-binding (CWB) domains, to be involved in different physiological functions that require bacterial cell wall remodeling. We identified a novel autolysin, Acd24020, from Clostridioides (Clostridium) difficile (C. difficile), with an endopeptidase catalytic domain belonging to the NlpC/P60 family and three bacterial Src-homology 3 domains as CWB domains. The catalytic domain of Acd24020 (Acd24020-CD) exhibited C. difficile-specific lytic activity equivalent to Acd24020, indicating that Acd24020-CD has full-function as a lytic enzyme by itself. To elucidate the specific peptidoglycan-recognition and catalytic reaction mechanisms of Acd24020-CD, biochemical characterization, X-ray structure determination, a modeling study of the enzyme/substrate complex, and mutagenesis analysis were performed. Acd24020-CD has an hourglass-shaped substrate-binding groove across the molecule, which is responsible for recognizing the direct 3-4 cross-linking structure unique to C. difficile peptidoglycan. Based on the X-ray structure and modeling study, we propose a dynamic Cys/His catalyzing mechanism, in which the catalytic Cys299 and His354 residues dynamically change their conformations to complement each step of the enzyme catalytic reaction.
Collapse
Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan.,Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan
| | - Jurina Kawasaki
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Kaho Murakami
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan
| |
Collapse
|
11
|
Tran SL, Cormontagne D, Vidic J, André-Leroux G, Ramarao N. Structural Modeling of Cell Wall Peptidase CwpFM (EntFM) Reveals Distinct Intrinsically Disordered Extensions Specific to Pathogenic Bacillus cereus Strains. Toxins (Basel) 2020; 12:toxins12090593. [PMID: 32937845 PMCID: PMC7551459 DOI: 10.3390/toxins12090593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022] Open
Abstract
The emergence of B. cereus as an opportunistic food-borne pathogen has intensified the need to distinguish strains of public health concern. The heterogeneity of the diseases associated with B. cereus infections emphasizes the versatility of these bacteria strains to colonize their host. Nevertheless, the molecular basis of these differences remains unclear. Several toxins are involved in virulence, particularly in gastrointestinal disorders, but there are currently no biological markers able to differentiate pathogenic from harmless strains. We have previously shown that CwpFM is a cell wall peptidase involved in B. cereus virulence. Here, we report a sequence/structure/function characterization of 39 CwpFM sequences, chosen from a collection of B. cereus with diverse virulence phenotypes, from harmless to highly pathogenic strains. CwpFM is homology-modeled in silico as an exported papain-like endopeptidase, with an N-terminal end composed of three successive bacterial Src Homology 3 domains (SH3b1–3) likely to control protein–protein interactions in signaling pathways, and a C-terminal end that contains a catalytic NLPC_P60 domain primed to form a competent active site. We confirmed in vitro that CwpFM is an endopeptidase with a moderate peptidoglycan hydrolase activity. Remarkably, CwpFMs from pathogenic strains harbor a specific stretch of twenty residues intrinsically disordered, inserted between the SH3b3 and the catalytic NLPC_P60 domain. This strongly suggests this linker as a marker of differentiation between B. cereus strains. We believe that our findings improve our understanding of the pathogenicity of B. cereus while advancing both clinical diagnosis and food safety.
Collapse
Affiliation(s)
- Seav-Ly Tran
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (S.-L.T.); (D.C.); (J.V.)
| | - Delphine Cormontagne
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (S.-L.T.); (D.C.); (J.V.)
| | - Jasmina Vidic
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (S.-L.T.); (D.C.); (J.V.)
| | - Gwenaëlle André-Leroux
- MaIAGE, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Correspondence: (G.A.-L.); (N.R.)
| | - Nalini Ramarao
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (S.-L.T.); (D.C.); (J.V.)
- Correspondence: (G.A.-L.); (N.R.)
| |
Collapse
|
12
|
Ega SL, Drendel G, Petrovski S, Egidi E, Franks AE, Muddada S. Comparative Analysis of Structural Variations Due to Genome Shuffling of Bacillus Subtilis VS15 for Improved Cellulase Production. Int J Mol Sci 2020; 21:ijms21041299. [PMID: 32075107 PMCID: PMC7072954 DOI: 10.3390/ijms21041299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/23/2022] Open
Abstract
Cellulose is one of the most abundant and renewable biomass products used for the production of bioethanol. Cellulose can be efficiently hydrolyzed by Bacillus subtilis VS15, a strain isolate obtained from decomposing logs. A genome shuffling approach was implemented to improve the cellulase activity of Bacillus subtilis VS15. Mutant strains were created using ethyl methyl sulfonate (EMS), N-Methyl-N′ nitro-N-nitrosoguanidine (NTG), and ultraviolet light (UV) followed by recursive protoplast fusion. After two rounds of shuffling, the mutants Gb2, Gc8, and Gd7 were produced that had an increase in cellulase activity of 128%, 148%, and 167%, respectively, in comparison to the wild type VS15. The genetic diversity of the shuffled strain Gd7 and wild type VS15 was compared at whole genome level. Genomic-level comparisons identified a set of eight genes, consisting of cellulase and regulatory genes, of interest for further analyses. Various genes were identified with insertions and deletions that may be involved in improved celluase production in Gd7. Strain Gd7 maintained the capability of hydrolyzing wheatbran to glucose and converting glucose to ethanol by fermentation with Saccharomyces cerevisiae of the wild type VS17. This ability was further confirmed by the acidified potassium dichromate (K2Cr2O7) method.
Collapse
Affiliation(s)
| | - Gene Drendel
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
| | - Eleonora Egidi
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW 2750, Australia
| | - Ashley E. Franks
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
- Centre for Future Landscapes, College of Science, Health and Engineering, La Trobe University, Melbourne, VI 3086, Australia
| | - Sudhamani Muddada
- Department of Biotechnology, K L E F University, Guntur 522 502, India;
- Correspondence: ; Tel.: +91-970-3470-598
| |
Collapse
|
13
|
Wangpaiboon K, Pitakchatwong C, Panpetch P, Charoenwongpaiboon T, Field RA, Pichyangkura R. Modified properties of alternan polymers arising from deletion of SH3-like motifs in Leuconostoc citreum ABK-1 alternansucrase. Carbohydr Polym 2019; 220:103-109. [PMID: 31196527 DOI: 10.1016/j.carbpol.2019.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 05/01/2019] [Accepted: 05/01/2019] [Indexed: 01/20/2023]
Abstract
Alternansucrase (ALT, EC 2.4.1.140) catalyses the formation of an alternating 〈-1, 3/1, 6-linked glucan, with periodic branch points, from sucrose substrate. Beyond the catalytic domain, this enzyme harbours seven additional C-terminal SH3-like repeats. We herein generated two truncated alternansucrases, possessing deletions of three and seven adjacent SH3 motifs, giving Δ3SHALT and Δ7SHALT. Δ3SHALT and Δ7SHALT exhibited kcat/Km for transglycosylation activity 2.3- and 1.5-fold lower than wild-type ALT (WTALT), while hydrolysis was detected only in the truncated ALTs, oligosaccharide patterns and polymer glycosidic linkage were similar to that of WTALT. The viscosities of ALT polymers increase by ˜100-fold at 15% (w/v), with gel-like states formed at 12.5, 15.0, and 20.0% (w/v) produced by polymer from WTALT, Δ3SHALT, and Δ7SHALT, respectively. The average nanoparticle sizes of Δ3SHALT and Δ7SHALT polymers were 80 nm, compared to 90 nm from WTALT. In conclusion, even relatively subtle differences in the structure of ALT-produced alternan give rise to profound impact on the glucan polymer physicochemical properties.
Collapse
Affiliation(s)
- Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Pawinee Panpetch
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| |
Collapse
|
14
|
Xu Q, Biancalana M, Grant JC, Chiu H, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger M, Deacon AM, Wilson IA. Structures of single-layer β-sheet proteins evolved from β-hairpin repeats. Protein Sci 2019; 28:1676-1689. [PMID: 31306512 PMCID: PMC6699103 DOI: 10.1002/pro.3683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 11/09/2022]
Abstract
Free-standing single-layer β-sheets are extremely rare in naturally occurring proteins, even though β-sheet motifs are ubiquitous. Here we report the crystal structures of three homologous, single-layer, anti-parallel β-sheet proteins, comprised of three or four twisted β-hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β-sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and are putatively involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent-exposed tyrosine residues, was identified on the concave surface of the β-sheet. These new modular single-layer β-sheet proteins may serve as a new model system for studying folding and design of β-rich proteins.
Collapse
Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics, www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator LaboratoryMenlo ParkCalifornia
- GMCA@APS, Argonne National LaboratoryLemontIllinois
| | - Matthew Biancalana
- Perlmutter Cancer Center, New York University Langone Medical Center, Smilow Research CenterNew YorkNew York
| | | | - Hsiu‐Ju Chiu
- Joint Center for Structural Genomics, www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator LaboratoryMenlo ParkCalifornia
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, www.jcsg.org
- Center for Research in Biological SystemsUniversity of CaliforniaLa JollaCalifornia
- Program on Bioinformatics and Systems BiologySanford‐Burnham Medical Research InstituteLa JollaCalifornia
- Division of Biomedical SciencesUniversity of CaliforniaRiversideCalifornia
| | - Mark W. Knuth
- Joint Center for Structural Genomics, www.jcsg.org
- Protein Sciences DepartmentGenomics Institute of the Novartis Research FoundationSan DiegoCalifornia
| | - Scott A. Lesley
- Joint Center for Structural Genomics, www.jcsg.org
- Protein Sciences DepartmentGenomics Institute of the Novartis Research FoundationSan DiegoCalifornia
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCalifornia
- Merck & Co., Inc.South San FranciscoCalifornia
| | - Adam Godzik
- Joint Center for Structural Genomics, www.jcsg.org
- Center for Research in Biological SystemsUniversity of CaliforniaLa JollaCalifornia
- Program on Bioinformatics and Systems BiologySanford‐Burnham Medical Research InstituteLa JollaCalifornia
- Division of Biomedical SciencesUniversity of CaliforniaRiversideCalifornia
| | - Marc‐André Elsliger
- Joint Center for Structural Genomics, www.jcsg.org
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCalifornia
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator LaboratoryMenlo ParkCalifornia
- Accelero BiostructuresSan CarlosCalifornia
| | - Ian A. Wilson
- Joint Center for Structural Genomics, www.jcsg.org
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCalifornia
| |
Collapse
|
15
|
Duchêne MC, Rolain T, Knoops A, Courtin P, Chapot-Chartier MP, Dufrêne YF, Hallet BF, Hols P. Distinct and Specific Role of NlpC/P60 Endopeptidases LytA and LytB in Cell Elongation and Division of Lactobacillus plantarum. Front Microbiol 2019; 10:713. [PMID: 31031721 PMCID: PMC6473061 DOI: 10.3389/fmicb.2019.00713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/21/2019] [Indexed: 11/22/2022] Open
Abstract
Peptidoglycan (PG) is an essential lattice of the bacterial cell wall that needs to be continuously remodeled to allow growth. This task is ensured by the concerted action of PG synthases that insert new material in the pre-existing structure and PG hydrolases (PGHs) that cleave the PG meshwork at critical sites for its processing. Contrasting with Bacillus subtilis that contains more than 35 PGHs, Lactobacillus plantarum is a non-sporulating rod-shaped bacterium that is predicted to possess a minimal set of 12 PGHs. Their role in morphogenesis and cell cycle remains mostly unexplored, except for the involvement of the glucosaminidase Acm2 in cell separation and the NlpC/P60 D, L-endopeptidase LytA in cell shape maintenance. Besides LytA, L. plantarum encodes three additional NlpC/P60 endopeptidases (i.e., LytB, LytC and LytD). The in silico analysis of these four endopeptidases suggests that they could have redundant functions based on their modular organization, forming two pairs of paralogous enzymes. In this work, we investigate the role of each Lyt endopeptidase in cell morphogenesis in order to evaluate their distinct or redundant functions, and eventually their synthetic lethality. We show that the paralogous LytC and LytD enzymes are not required for cell shape maintenance, which may indicate an accessory role such as in PG recycling. In contrast, LytA and LytB appear to be key players of the cell cycle. We show here that LytA is required for cell elongation while LytB is involved in the spatio-temporal regulation of cell division. In addition, both PGHs are involved in the proper positioning of the division site. The absence of LytA activity is responsible for the asymmetrical positioning of septa in round cells while the lack of LytB results in a lateral misplacement of division planes in rod-shaped cells. Finally, we show that the co-inactivation of LytA and LytB is synthetically affecting cell growth, which confirms the key roles played by both enzymes in PG remodeling during the cell cycle of L. plantarum. Based on the large distribution of NlpC/P60 endopeptidases in low-GC Gram-positive bacteria, these enzymes are attractive targets for the discovery of novel antimicrobial compounds.
Collapse
Affiliation(s)
- Marie-Clémence Duchêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Thomas Rolain
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Adrien Knoops
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Pascal Courtin
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Bernard F Hallet
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Pascal Hols
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| |
Collapse
|
16
|
Kim B, Wang YC, Hespen CW, Espinosa J, Salje J, Rangan KJ, Oren DA, Kang JY, Pedicord VA, Hang HC. Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis. eLife 2019; 8:e45343. [PMID: 30969170 PMCID: PMC6483599 DOI: 10.7554/elife.45343] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
We discovered that Enterococcus faecium (E. faecium), a ubiquitous commensal bacterium, and its secreted peptidoglycan hydrolase (SagA) were sufficient to enhance intestinal barrier function and pathogen tolerance, but the precise biochemical mechanism was unknown. Here we show E. faecium has unique peptidoglycan composition and remodeling activity through SagA, which generates smaller muropeptides that more effectively activates nucleotide-binding oligomerization domain-containing protein 2 (NOD2) in mammalian cells. Our structural and biochemical studies show that SagA is a NlpC/p60-endopeptidase that preferentially hydrolyzes crosslinked Lys-type peptidoglycan fragments. SagA secretion and NlpC/p60-endopeptidase activity was required for enhancing probiotic bacteria activity against Clostridium difficile pathogenesis in vivo. Our results demonstrate that the peptidoglycan composition and hydrolase activity of specific microbiota species can activate host immune pathways and enhance tolerance to pathogens.
Collapse
Affiliation(s)
- Byungchul Kim
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Yen-Chih Wang
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Charles W Hespen
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Jeanne Salje
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Kavita J Rangan
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Deena A Oren
- Structural Biology Resource CenterThe Rockefeller UniversityNew YorkUnited States
| | - Jin Young Kang
- Laboratory of Molecular BiophysicsThe Rockefeller UniversityNew YorkUnited States
| | - Virginia A Pedicord
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUnited Kingdom
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| |
Collapse
|
17
|
Pinheiro J, Biboy J, Vollmer W, Hirt RP, Keown JR, Artuyants A, Black MM, Goldstone DC, Simoes-Barbosa A. The Protozoan Trichomonas vaginalis Targets Bacteria with Laterally Acquired NlpC/P60 Peptidoglycan Hydrolases. mBio 2018; 9:e01784-18. [PMID: 30538181 PMCID: PMC6299479 DOI: 10.1128/mbio.01784-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/01/2018] [Indexed: 02/01/2023] Open
Abstract
The human eukaryotic pathogen Trichomonas vaginalis causes trichomoniasis, a prevalent sexually transmitted infection. This extracellular protozoan is intimately associated with the human vaginal mucosa and microbiota, but key aspects of the complex interactions between the parasite and the vaginal bacteria remain elusive. We report that T. vaginalis has acquired, by lateral gene transfer from bacteria, genes encoding peptidoglycan hydrolases of the NlpC/P60 family. Two of the T. vaginalis enzymes were active against bacterial peptidoglycan, retaining the active-site fold and specificity as dl-endopeptidases. The endogenous NlpC/P60 genes are transcriptionally upregulated in T. vaginalis in the presence of bacteria. The overexpression of an exogenous copy enables the parasite to outcompete bacteria from mixed cultures, consistent with the biochemical activity of the enzyme. Our study results highlight the relevance of the interactions of this eukaryotic pathogen with bacteria, a poorly understood aspect of the biology of this important human parasite.IMPORTANCETrichomonas vaginalis is a parasitic protozoan of the human urogenital tract that causes trichomoniasis, a very common sexually transmitted disease. Despite residing extracellularly and in close association with the vaginal bacteria (i.e., the microbiota), very little is known about the nature of the parasite-bacterium interactions. Our study showed that this parasite had acquired genes from bacteria which retained their original function. They produce active enzymes capable of degrading peptidoglycan, a unique polymer of the bacterial cell envelope, helping the parasite to outcompete bacteria in mixed cultures. This study was the first to show that a laterally acquired group of genes enables a eukaryotic mucosal pathogen to control bacterial population. We highlight the importance of understanding the interactions between pathogens and microbiota, as the outcomes of these interactions are increasingly understood to have important implications on health and disease.
Collapse
Affiliation(s)
- Jully Pinheiro
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert P Hirt
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jeremy R Keown
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Moyra M Black
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | | |
Collapse
|
18
|
Solution scattering study of the Bacillus subtilis PgdS enzyme involved in poly-γ-glutamic acids degradation. PLoS One 2018; 13:e0195355. [PMID: 29608608 PMCID: PMC5880399 DOI: 10.1371/journal.pone.0195355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
The PgdS enzyme is a poly-γ-glutamic (γ-PGA) hydrolase, which has potential application for a controllable degradation of γ-PGA by enzymatic depolymerization; however, the structure of PgdS is still unknown. Here, to study in detail the full-length PgdS structure, we analyze the low-resolution architecture of PgdS hydrolase from Bacillus subtilis in solution using small angle X-ray scattering (SAXS) method. Combining with other methods, like dynamic light scattering and mutagenesis analyses, a model for the full length structure and the possible substrate delivery route of PgdS are proposed. The results will provide useful hints for future investigations into the mechanisms of γ-PGA degradation by the PgdS hydrolase and may provide valuable practical information.
Collapse
|
19
|
A New Essential Cell Division Protein in Caulobacter crescentus. J Bacteriol 2017; 199:JB.00811-16. [PMID: 28167520 DOI: 10.1128/jb.00811-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/31/2017] [Indexed: 11/20/2022] Open
Abstract
Bacterial cell division is a complex process that relies on a multiprotein complex composed of a core of widely conserved and generally essential proteins and on accessory proteins that vary in number and identity in different bacteria. The assembly of this complex and, particularly, the initiation of constriction are regulated processes that have come under intensive study. In this work, we characterize the function of DipI, a protein conserved in Alphaproteobacteria and Betaproteobacteria that is essential in Caulobacter crescentus Our results show that DipI is a periplasmic protein that is recruited late to the division site and that it is required for the initiation of constriction. The recruitment of the conserved cell division proteins is not affected by the absence of DipI, but localization of DipI to the division site occurs only after a mature divisome has formed. Yeast two-hybrid analysis showed that DipI strongly interacts with the FtsQLB complex, which has been recently implicated in regulating constriction initiation. A possible role of DipI in this process is discussed.IMPORTANCE Bacterial cell division is a complex process for which most bacterial cells assemble a multiprotein complex that consists of conserved proteins and of accessory proteins that differ among bacterial groups. In this work, we describe a new cell division protein (DipI) present only in a group of bacteria but essential in Caulobacter crescentus Cells devoid of DipI cannot constrict. Although a mature divisome is required for DipI recruitment, DipI is not needed for recruiting other division proteins. These results, together with the interaction of DipI with a protein complex that has been suggested to regulate cell wall synthesis during division, suggest that DipI may be part of the regulatory mechanism that controls constriction initiation.
Collapse
|
20
|
Yu M, Yang J, Guo M. Is the LysM domain of L. monocytogenes p60 protein suitable for engineering a protein with high peptidoglycan binding affinity? Bioengineered 2016; 7:406-410. [PMID: 27333274 DOI: 10.1080/21655979.2016.1200772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Lysin motif (LysM) is a highly conserved carbohydrate binding module that is widely present in proteins from both prokaryotes and eukaryotes. LysM domains from many LysM-containing proteins can be taken out of their natural context and retain their ability to bind peptidoglycan. Therefore, LysM has enormous potential for applications in both industry and medicine. This potential has stimulated an intensive search for LysM modules with different evolutionary origins. The p60 protein (Lm-p60) is an NlpC/P60-containing peptidoglycan hydrolase secreted by Listeria monocytogenes. The N-terminus of Lm-p60 contains 2 LysM modules separated by an SH3 module. Our recent study of Lm-p60 demonstrates that the N-terminal half of Lm-p60, comprised of 2 LysM and 1 SH3 module, is able to recognize and bind peptidoglycan. The LysM domain of Lm-p60 contains only 2 LysM modules, which is the minimum number of LysM modules in most NlpC/P60-containing proteins, but it shows strong affinity for peptidoglycan. Moreover, these 2 LysM modules have only 38.64% similarity to each other. These data allowed us to conclude that the 2 LysM modules from Lm-p60 have different evolutionary origins, suggesting that they are suitable candidate peptidoglycan-binding modules for protein engineering in order to create a protein with a high binding affinity to peptidoglycan.
Collapse
Affiliation(s)
- Minfeng Yu
- a College of Bioscience and Biotechnology, Yangzhou University , Yangzhou City, Jiangsu , PR China
| | - Jing Yang
- a College of Bioscience and Biotechnology, Yangzhou University , Yangzhou City, Jiangsu , PR China
| | - Minliang Guo
- a College of Bioscience and Biotechnology, Yangzhou University , Yangzhou City, Jiangsu , PR China
| |
Collapse
|
21
|
Bannantine JP, Lingle CK, Adam PR, Ramyar KX, McWhorter WJ, Stabel JR, Picking WD, Geisbrecht BV. NlpC/P60 domain-containing proteins of Mycobacterium avium subspecies paratuberculosis that differentially bind and hydrolyze peptidoglycan. Protein Sci 2016; 25:840-51. [PMID: 26799947 DOI: 10.1002/pro.2884] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/14/2016] [Accepted: 01/19/2016] [Indexed: 01/22/2023]
Abstract
A subset of proteins containing NlpC/P60 domains are bacterial peptidoglycan hydrolases that cleave noncanonical peptide linkages and contribute to cell wall remodeling as well as cell separation during late stages of division. Some of these proteins have been shown to cleave peptidoglycan in Mycobacterium tuberculosis and play a role in Mycobacterium marinum virulence of zebra fish; however, there are still significant knowledge gaps concerning the molecular function of these proteins in Mycobacterium avium subspecies paratuberculosis (MAP). The MAP genome sequence encodes five NlpC/P60 domain-containing proteins. We describe atomic resolution crystal structures of two such MAP proteins, MAP_1272c and MAP_1204. These crystal structures, combined with functional assays to measure peptidoglycan cleavage activity, led to the observation that MAP_1272c does not have a functional catalytic core for peptidoglycan hydrolysis. Furthermore, the structure and sequence of MAP_1272c demonstrate that the catalytic residues normally required for hydrolysis are absent, and the protein does not bind peptidoglycan as efficiently as MAP_1204. While the NlpC/P60 catalytic triad is present in MAP_1204, changing the catalytic cysteine-155 residue to a serine significantly diminished catalytic activity, but did not affect binding to peptidoglycan. Collectively, these findings suggest a broader functional repertoire for NlpC/P60 domain-containing proteins than simply hydrolases.
Collapse
Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa
| | - Cari K Lingle
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - Philip R Adam
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma
| | - Kasra X Ramyar
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - William J McWhorter
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - Judith R Stabel
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa
| | - William D Picking
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma
| | - Brian V Geisbrecht
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| |
Collapse
|
22
|
House dust mites possess a polymorphic, single domain putative peptidoglycan d,l endopeptidase belonging to the NlpC/P60 Superfamily. FEBS Open Bio 2015; 5:813-23. [PMID: 26566476 PMCID: PMC4600878 DOI: 10.1016/j.fob.2015.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/08/2015] [Accepted: 09/10/2015] [Indexed: 11/23/2022] Open
Abstract
A 14 kDa protein homologous to the γ-d-glutamyl-l-diamino acid endopeptidase members of the NlpC/P60 Superfamily has been described in Dermatophagoides pteronyssinus and Dermatophagoides farinae but it is not clear whether other species produce homologues. Bioinformatics revealed homologous genes in other Sarcopteformes mite species (Psoroptes ovis and Blomia tropicalis) but not in Tetranychus urticae and Metaseiulus occidentalis. The degrees of identity (similarity) between the D. pteronyssinus mature protein and those from D. farinae, P. ovis and B. tropicalis were 82% (96%), 77% (93%) and 61% (82%), respectively. Phylogenetic studies showed the mite proteins were monophyletic and shared a common ancestor with both actinomycetes and ascomycetes. The gene encoding the D. pteronyssinus protein was polymorphic and intronless in contrast to that reported for D. farinae. Homology studies suggest that the mite, ascomycete and actinomycete proteins are involved in the catalysis of stem peptide attached to peptidoglycan. The finding of a gene encoding a P60 family member in the D. pteronyssinus genome together with the presence of a bacterial promotor suggests an evolutionary link to one or more prokaryotic endosymbionts.
Collapse
|
23
|
Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains. mBio 2015; 6:e02327-14. [PMID: 26374125 PMCID: PMC4600125 DOI: 10.1128/mbio.02327-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (or dl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l-Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.
Collapse
|
24
|
Domain function dissection and catalytic properties of Listeria monocytogenes p60 protein with bacteriolytic activity. Appl Microbiol Biotechnol 2015; 99:10527-37. [PMID: 26363556 DOI: 10.1007/s00253-015-6967-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/12/2015] [Accepted: 08/23/2015] [Indexed: 02/07/2023]
Abstract
The major extracellular protein p60 of Listeria monocytogenes (Lm-p60) is an autolysin that can hydrolyze the peptidoglycan of bacterial cell wall and has been shown to be required for L. monocytogenes virulence. The predicted three-dimensional structure of Lm-p60 showed that Lm-p60 could be split into two independent structural domains at the amino acid residue 270. Conserved motif analysis showed that V30, D207, S395, and H444 are the key amino acid residues of the corresponding motifs. However, not only the actual functions of these two domains but also the catalytic properties of Lm-p60 are unclear. We try to express recombinant Lm-p60 and identify the functions of two domains by residue substitution (V30A, D207A, S395A, and H444A) and peptide truncation. The C-terminal domain was identified as catalytic element and N-terminal domain as substrate recognition and binding element. Either N-terminal domain truncation or C-terminal domain truncation presents corresponding biological activity. The catalytic activity of Lm-p60 with a malfunctioned substrate-binding domain was decreased, while the substrate binding was not affected by a mulfunctioned catalytic domain. With turbidimetric method, we determined the optimal conditions for the bacteriolytic activity of Lm-p60 against Micrococcus lysodeikficus. The assay for the effect of Lm-p60 on the bacteriolytic activity of lysozyme revealed that the combined use of Lm-p60 protein with lysozyme showed a strong synergistic effect on the bacteriolytic activity.
Collapse
|
25
|
Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist. Proc Natl Acad Sci U S A 2015; 112:E4825-34. [PMID: 26283367 DOI: 10.1073/pnas.1508737112] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The trillions of bacteria that make up the human microbiome are believed to encode functions that are important to human health; however, little is known about the specific effectors that commensal bacteria use to interact with the human host. Functional metagenomics provides a systematic means of surveying commensal DNA for genes that encode effector functions. Here, we examine 3,000 Mb of metagenomic DNA cloned from three phenotypically distinct patients for effectors that activate NF-κB, a transcription factor known to play a central role in mediating responses to environmental stimuli. This screen led to the identification of 26 unique commensal bacteria effector genes (Cbegs) that are predicted to encode proteins with diverse catabolic, anabolic, and ligand-binding functions and most frequently interact with either glycans or lipids. Detailed analysis of one effector gene family (Cbeg12) recovered from all three patient libraries found that it encodes for the production of N-acyl-3-hydroxypalmitoyl-glycine (commendamide). This metabolite was also found in culture broth from the commensal bacterium Bacteroides vulgatus, which harbors a gene highly similar to Cbeg12. Commendamide resembles long-chain N-acyl-amides that function as mammalian signaling molecules through activation of G-protein-coupled receptors (GPCRs), which led us to the observation that commendamide activates the GPCR G2A/GPR132. G2A has been implicated in disease models of autoimmunity and atherosclerosis. This study shows the utility of functional metagenomics for identifying potential mechanisms used by commensal bacteria for host interactions and outlines a functional metagenomics-based pipeline for the systematic identification of diverse commensal bacteria effectors that impact host cellular functions.
Collapse
|
26
|
Roy U, Chalasani AG, Shekh MR. The anti-Candida activity by Ancillary Proteins of an Enterococcus faecium strain. Front Microbiol 2015; 6:339. [PMID: 26005434 PMCID: PMC4424852 DOI: 10.3389/fmicb.2015.00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/06/2015] [Indexed: 11/13/2022] Open
Abstract
An antimycotic activity toward seven strains of Candida albicans was demonstrated erstwhile by a wild-type Enterococcus faecium isolated from a penguin rookery of the Antarctic region. In the present study the antimicrobial principle was purified by ion exchange and gel permeation chromatography and further was analyzed by LC-ESI-MS/MS. In the purification steps, the dialyzed concentrate and ion exchange fractions inhibited C. albicans MTCC 3958, 183, and SC 5314. However, the gel filtration purified fractions inhibited MTCC 3958 and 183. The data obtained from the LC-ESI-MS/MS indicate that the antimicrobial activity of the anti-Candida protein produced by E. faecium is facilitated by Sag A/Bb for the binding of the indicator organism's cell membrane. Partial N-terminal sequence revealed 12 N-terminal amino acid residues and its analysis shown that it belongs to the LysM motif. The nucleotide sequence of PCR-amplified product could detect 574 nucleotides of the LysM gene responsible for binding to chitin of the cell wall of Candida sp.
Collapse
Affiliation(s)
- Utpal Roy
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani KK Birla Goa Campus Vasco Da Gama, India
| | - Ajay G Chalasani
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani KK Birla Goa Campus Vasco Da Gama, India
| | - M Raeesh Shekh
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani KK Birla Goa Campus Vasco Da Gama, India
| |
Collapse
|
27
|
Wong JEMM, Midtgaard SR, Gysel K, Thygesen MB, Sørensen KK, Jensen KJ, Stougaard J, Thirup S, Blaise M. An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:592-605. [PMID: 25760608 PMCID: PMC4356369 DOI: 10.1107/s139900471402793x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/22/2014] [Indexed: 11/10/2022]
Abstract
LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.
Collapse
Affiliation(s)
- Jaslyn E. M. M. Wong
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Søren Roi Midtgaard
- Niels Bohr Institute, Faculty of Science, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Kira Gysel
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Mikkel B. Thygesen
- Centre for Carbohydrate Recognition and Signalling, Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Kasper K. Sørensen
- Centre for Carbohydrate Recognition and Signalling, Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Knud J. Jensen
- Centre for Carbohydrate Recognition and Signalling, Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Søren Thirup
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Mickaël Blaise
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| |
Collapse
|
28
|
Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family. Structure 2014; 22:1799-1809. [PMID: 25465128 DOI: 10.1016/j.str.2014.09.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 01/01/2023]
Abstract
GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo structure at 1.15 Å resolution shows that AmiA is related to NlpC/P60 γ-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and subsequently were characterized experimentally. Further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines another amidase family.
Collapse
|
29
|
Xu Q, Deller MC, Nielsen TK, Grant JC, Lesley SA, Elsliger MA, Deacon AM, Wilson IA. Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin. PLoS One 2014; 9:e107309. [PMID: 25197798 PMCID: PMC4157861 DOI: 10.1371/journal.pone.0107309] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/09/2014] [Indexed: 01/15/2023] Open
Abstract
Kanadaptin is a nuclear protein of unknown function that is widely expressed in mammalian tissues. The crystal structure of the forkhead-associated (FHA) domain of human kanadaptin was determined to 1.6 Å resolution. The structure reveals an asymmetric dimer in which one monomer is complexed with a phosphopeptide mimic derived from a peptide segment from the N-terminus of a symmetry-related molecule as well as a sulfate bound to the structurally conserved phosphothreonine recognition cleft. This structure provides insights into the molecular recognition features utilized by this family of proteins and represents the first evidence that kanadaptin is likely involved in a phosphorylation-mediated signaling pathway. These results will be of use for designing experiments to further probe the function of kanadaptin.
Collapse
Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Marc C. Deller
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tine K. Nielsen
- Protein Production Facility, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joanna C. Grant
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Scott A. Lesley
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Ian A. Wilson
- Joint Center for Structural Genomics, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
30
|
Squeglia F, Ruggiero A, Romano M, Vitagliano L, Berisio R. Mutational and structural study of RipA, a key enzyme in Mycobacterium tuberculosis cell division: evidence for the L-to-D inversion of configuration of the catalytic cysteine. ACTA ACUST UNITED AC 2014; 70:2295-300. [PMID: 25195744 DOI: 10.1107/s1399004714013674] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/11/2014] [Indexed: 11/10/2022]
Abstract
RipA is a key cysteine protease of Mycobacterium tuberculosis as it is responsible for bacterial daughter-cell separation. Although it is an important target for antimicrobial development, its mechanism of action and its interaction pattern with its substrate are hitherto unknown. By combining crystallographic and mutational studies with functional assays and molecular modelling, it is shown that the catalytic activity of the enzyme relies on a Cys-His-Glu triad and the impact of the mutation of each residue of the triad on the structure and function of RipA is analysed. Unexpectedly, the crystallographic analyses reveal that mutation of the glutamic acid to alanine results in inversion of the configuration of the catalytic cysteine. The consequent burial of the catalytic cysteine side chain explains the enzyme inactivation upon mutation. These data point to a novel role of the acidic residue often present in the triad of cysteine proteases as a supervisor of cysteine configuration through preservation of the local structural integrity.
Collapse
Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Maria Romano
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| |
Collapse
|
31
|
Sanz-Gaitero M, Keary R, Garcia-Doval C, Coffey A, van Raaij MJ. Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K. Virol J 2014; 11:133. [PMID: 25064136 PMCID: PMC4126393 DOI: 10.1186/1743-422x-11-133] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteriophages encode endolysins to lyse their host cell and allow escape of their progeny. Endolysins are also active against Gram-positive bacteria when applied from the outside and are thus attractive anti-bacterial agents. LysK, an endolysin from staphylococcal phage K, contains an N-terminal cysteine-histidine dependent amido-hydrolase/peptidase domain (CHAP(K)), a central amidase domain and a C-terminal SH3b cell wall-binding domain. CHAP(K) cleaves bacterial peptidoglycan between the tetra-peptide stem and the penta-glycine bridge. METHODS The CHAP(K) domain of LysK was crystallized and high-resolution diffraction data was collected both from a native protein crystal and a methylmercury chloride derivatized crystal. The anomalous signal contained in the derivative data allowed the location of heavy atom sites and phase determination. The resulting structures were completed, refined and analyzed. The presence of calcium and zinc ions in the structure was confirmed by X-ray fluorescence emission spectroscopy. Zymogram analysis was performed on the enzyme and selected site-directed mutants. RESULTS The structure of CHAP(K) revealed a papain-like topology with a hydrophobic cleft, where the catalytic triad is located. Ordered buffer molecules present in this groove may mimic the peptidoglycan substrate. When compared to previously solved CHAP domains, CHAP(K) contains an additional lobe in its N-terminal domain, with a structural calcium ion, coordinated by residues Asp45, Asp47, Tyr49, His51 and Asp56. The presence of a zinc ion in the active site was also apparent, coordinated by the catalytic residue Cys54 and a possible substrate analogue. Site-directed mutagenesis was used to demonstrate that residues involved in calcium binding and of the proposed active site were important for enzyme activity. CONCLUSIONS The high-resolution structure of the CHAP(K) domain of LysK was determined, suggesting the location of the active site, the substrate-binding groove and revealing the presence of a structurally important calcium ion. A zinc ion was found more loosely bound. Based on the structure, we propose a possible reaction mechanism. Future studies will be aimed at co-crystallizing CHAP(K) with substrate analogues and elucidating its role in the complete LysK protein. This, in turn, may lead to the design of site-directed mutants with altered activity or substrate specificity.
Collapse
Affiliation(s)
| | | | | | | | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain.
| |
Collapse
|
32
|
RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function. Biochem J 2013; 457:33-41. [DOI: 10.1042/bj20131227] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RipD from Mycobacterium tuberculosis represents the first NlpC/p60 domain protein that evolved a non-catalytic cell wall binding function. The structure of the NlpC/p60 domain is presented in this study and the protein is characterized with respect to catalytic activity and peptidoglycan binding.
Collapse
|
33
|
Wong JEMM, Blaise M. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the putative NlpC/P60 endopeptidase, TTHA0266, from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1291-4. [PMID: 24192372 PMCID: PMC3818056 DOI: 10.1107/s1744309113027164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/02/2013] [Indexed: 11/10/2022]
Abstract
Autolysins belong to a protein family involved in peptidoglycan degradation and remodelling. Within this family, NlpC/P60 endopeptidases are involved in the hydrolysis of the peptide arm of peptidoglycan. In this work, the putative NlpC/P60 endopeptidase TTHA0266 from Thermus thermophilus HB8 was overexpressed, purified and crystallized. The crystals diffracted to 2.4 Å resolution and belonged to the hexagonal space group P6(1), with unit-cell parameters a = b = 71.19, c = 198.68 Å, γ = 120°. Selenomethionine-substituted protein was crystallized and the structure was solved by single-wavelength anomalous dispersion.
Collapse
Affiliation(s)
- Jaslyn E. M. M. Wong
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus, Denmark
| | - Mickael Blaise
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus, Denmark
| |
Collapse
|
34
|
Xu Q, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Structures of a bifunctional cell wall hydrolase CwlT containing a novel bacterial lysozyme and an NlpC/P60 DL-endopeptidase. J Mol Biol 2013; 426:169-84. [PMID: 24051416 DOI: 10.1016/j.jmb.2013.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 11/17/2022]
Abstract
Tn916-like conjugative transposons carrying antibiotic resistance genes are found in a diverse range of bacteria. Orf14 within the conjugation module encodes a bifunctional cell wall hydrolase CwlT that consists of an N-terminal bacterial lysozyme domain (N-acetylmuramidase, bLysG) and a C-terminal NlpC/P60 domain (γ-d-glutamyl-l-diamino acid endopeptidase) and is expected to play an important role in the spread of the transposons. We determined the crystal structures of CwlT from two pathogens, Staphylococcus aureus Mu50 (SaCwlT) and Clostridium difficile 630 (CdCwlT). These structures reveal that NlpC/P60 and LysG domains are compact and conserved modules, connected by a short flexible linker. The LysG domain represents a novel family of widely distributed bacterial lysozymes. The overall structure and the active site of bLysG bear significant similarity to other members of the glycoside hydrolase family 23 (GH23), such as the g-type lysozyme (LysG) and Escherichia coli lytic transglycosylase MltE. The active site of bLysG contains a unique structural and sequence signature (DxxQSSES+S) that is important for coordinating a catalytic water. Molecular modeling suggests that the bLysG domain may recognize glycan in a similar manner to MltE. The C-terminal NlpC/P60 domain contains a conserved active site (Cys-His-His-Tyr) that appears to be specific to murein tetrapeptide. Access to the active site is likely regulated by isomerism of a side chain atop the catalytic cysteine, allowing substrate entry or product release (open state), or catalysis (closed state).
Collapse
Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Carol L Farr
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics (http://www.jcsg.org); Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark W Knuth
- Joint Center for Structural Genomics (http://www.jcsg.org); Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Mitchell D Miller
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Scott A Lesley
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Adam Godzik
- Joint Center for Structural Genomics (http://www.jcsg.org); Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ashley M Deacon
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ian A Wilson
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
35
|
Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3. Biochem J 2013; 454:59-68. [DOI: 10.1042/bj20130193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The recently described T6SS (type VI secretion system) acts as a needle that punctures the membrane of the target cells to deliver effector proteins. Type VI amidase effectors can be classified into four divergent families (Tae1–Tae4). These effectors are secreted into the periplasmic space of neighbouring cells via the T6SS and subsequently rupture peptidoglycan. However, the donor cells are protected from damage because of the presence of their cognate immunity proteins [Tai1 (type VI amidase immunity 1)–Tai4]. In the present paper, we describe the structure of Tae3 in complex with Tai3. The Tae3–Tai3 complex exists as a stable heterohexamer, which is composed of two Tae3 molecules and two Tai3 homodimers (Tae3–Tai34–Tae3). Tae3 shares a common NlpC/P60 fold, which consists of N-terminal and C-terminal subdomains. Structural analysis indicates that two unique loops around the catalytic cleft adopt a closed conformation, resulting in a narrow and extended groove involved in the binding of the substrate. The inhibition of Tae3 is attributed to the insertion of the Ω-loop (loop of α3–α4) of Tai3 into the catalytic groove. Furthermore, a cell viability assay confirmed that a conserved motif (Gln-Asp-Xaa) in Tai3 members may play a key role in the inhibition process. Taken together, the present study has revealed a novel inhibition mechanism and provides insights into the role played by T6SS in interspecific competition.
Collapse
|
36
|
Benz J, Reinstein J, Meinhart A. Structural Insights into the Effector - Immunity System Tae4/Tai4 from Salmonella typhimurium. PLoS One 2013; 8:e67362. [PMID: 23826277 PMCID: PMC3695027 DOI: 10.1371/journal.pone.0067362] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/17/2013] [Indexed: 11/19/2022] Open
Abstract
Type-6-secretion systems of Gram-negative bacteria are widely distributed needle-like multi-protein complexes that are involved in microbial defense mechanisms. During bacterial competition these injection needles dispense effector proteins into the periplasm of competing bacteria where they induce degradation of the peptidoglycan scaffold and lead to cell lysis. Donor cells co-produce immunity proteins and shuttle them into their own periplasm to prevent accidental toxication by siblings. Recently, a plethora of previously unidentified hydrolases have been suggested to be peptidoglycan degrading amidases. These hydrolases are part of effector/immunity pairs that have been associated with bacterial warfare by type-6-secretion systems. The Tae4 and Tai4 operon encoded by Salmonella typhimurium is one of these newly discovered effector/immunity pairs. The Tae4 effector proteins induce cell lysis by cleaving the γ-D-glutamyl-L-meso-diaminopimelic acid amide bond of acceptor stem muropeptides of the Gram-negative peptidoglycan. Although homologues of the Tae4/Tai4 system have been identified in various different pathogens, little is known about the functional mechanism of effector protein activity and their inhibition by the cognate immunity proteins. Here, we present the high-resolution crystal structure of the effector Tae4 of S. typhimurium in complex with its immunity protein Tai4. We show that Tae4 contains a classical NlpC/P60-peptidase core which is common to other effector proteins of the type-6-secretion system. However, Tae4 has unique structural features that are exclusively conserved within the family of Tae4 effectors and which are important for the substrate specificity. Most importantly, we show that although the overall structure of Tai4 is different to previously described immunity proteins, the essential mode of enzyme inhibition is conserved. Additionally, we provide evidence that inhibition in the Tae4/Tai4 heterotetramer relies on a central Tai4 dimer in order to acquire functionality.
Collapse
Affiliation(s)
- Juliane Benz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
- * E-mail:
| |
Collapse
|
37
|
Rolain T, Bernard E, Beaussart A, Degand H, Courtin P, Egge-Jacobsen W, Bron PA, Morsomme P, Kleerebezem M, Chapot-Chartier MP, Dufrêne YF, Hols P. O-glycosylation as a novel control mechanism of peptidoglycan hydrolase activity. J Biol Chem 2013; 288:22233-47. [PMID: 23760506 DOI: 10.1074/jbc.m113.470716] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acm2, the major autolysin of Lactobacillus plantarum, is a tripartite protein. Its catalytic domain is surrounded by an O-glycosylated N-terminal region rich in Ala, Ser, and Thr (AST domain), which is of low complexity and unknown function, and a C-terminal region composed of five SH3b peptidoglycan (PG) binding domains. Here, we investigate the contribution of these two accessory domains and of O-glycosylation to Acm2 functionality. We demonstrate that Acm2 is an N-acetylglucosaminidase and identify the pattern of O-glycosylation (21 mono-N-acetylglucosamines) of its AST domain. The O-glycosylation process is species-specific as Acm2 purified from Lactococcus lactis is not glycosylated. We therefore explored the functional role of O-glycosylation by purifying different truncated versions of Acm2 that were either glycosylated or non-glycosylated. We show that SH3b domains are able to bind PG and are responsible for Acm2 targeting to the septum of dividing cells, whereas the AST domain and its O-glycosylation are not involved in this process. Notably, our data reveal that the lack of O-glycosylation of the AST domain significantly increases Acm2 enzymatic activity, whereas removal of SH3b PG binding domains dramatically reduces this activity. Based on this antagonistic role, we propose a model in which access of the Acm2 catalytic domain to its substrate may be hindered by the AST domain where O-glycosylation changes its conformation and/or mediates interdomain interactions. To the best of our knowledge, this is the first time that O-glycosylation is shown to control the activity of a bacterial enzyme.
Collapse
Affiliation(s)
- Thomas Rolain
- Institut des Sciences de la Vie, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
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: 13.5] [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
|
39
|
MpaA is a murein-tripeptide-specific zinc carboxypeptidase that functions as part of a catabolic pathway for peptidoglycan-derived peptides in γ-proteobacteria. Biochem J 2013; 448:329-41. [PMID: 22970852 DOI: 10.1042/bj20121164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The murein peptide amidase MpaA is a cytoplasmic enzyme that processes peptides derived from the turnover of murein. We have purified the enzyme from Escherichia coli and demonstrated that it efficiently hydrolyses the γ-D-glutamyl-diaminopimelic acid bond in the murein tripeptide (L-Ala-γ-D-Glu-meso-Dap), with Km and kcat values of 0.41±0.05 mM and 38.3±10 s-1. However, it is unable to act on the murein tetrapeptide (L-Ala-γ-D-Glu-meso-Dap-D-Ala). E. coli MpaA is a homodimer containing one bound zinc ion per chain, as judged by mass spectrometric analysis and size-exclusion chromatography. To investigate the structure of MpaA we solved the crystal structure of the orthologous protein from Vibrio harveyi to 2.17 Å (1Å=0.1 nm). Vh_MpaA, which has identical enzymatic and biophysical properties to the E. coli enzyme, has high structural similarity to eukaryotic zinc carboxypeptidases. The structure confirms that MpaA is a dimeric zinc metalloprotein. Comparison of the structure of MpaA with those of other carboxypeptidases reveals additional structure that partially occludes the substrate-binding groove, perhaps explaining the narrower substrate specificity of the enzyme compared with other zinc carboxypeptidases. In γ-proteobacteria mpaA is often located adjacent to mppA which encodes a periplasmic transporter protein previously shown to bind murein tripeptide. We demonstrate that MppA can also bind murein tetrapeptide with high affinity. The genetic coupling of these genes and their related biochemical functions suggest that MpaA amidase and MppA transporter form part of a catabolic pathway for utilization of murein-derived peptides that operates in γ-proteobacteria in addition to the established murein recycling pathways.
Collapse
|
40
|
Zhang H, Zhang H, Gao ZQ, Wang WJ, Liu GF, Xu JH, Su XD, Dong YH. Structure of the type VI effector-immunity complex (Tae4-Tai4) provides novel insights into the inhibition mechanism of the effector by its immunity protein. J Biol Chem 2013; 288:5928-39. [PMID: 23288853 DOI: 10.1074/jbc.m112.434357] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The type VI secretion system (T6SS), a multisubunit needle-like apparatus, has recently been found to play a role in interspecies interactions. The gram-negative bacteria harboring T6SS (donor) deliver the effectors into their neighboring cells (recipient) to kill them. Meanwhile, the cognate immunity proteins were employed to protect the donor cells against the toxic effectors. Tae4 (type VI amidase effector 4) and Tai4 (type VI amidase immunity 4) are newly identified T6SS effector-immunity pairs. Here, we report the crystal structures of Tae4 from Enterobacter cloacae and Tae4-Tai4 complexes from both E. cloacae and Salmonella typhimurium. Tae4 acts as a DL-endopeptidase and displays a typical N1pC/P60 domain. Unlike Tsi1 (type VI secretion immunity 1), Tai4 is an all-helical protein and forms a dimer in solution. The small angle x-ray scattering study combined with the analytical ultracentrifugation reveal that the Tae4-Tai4 complex is a compact heterotetramer that consists of a Tai4 dimer and two Tae4 molecules in solution. Structure-based mutational analysis of the Tae4-Tai4 interface shows that a helix (α3) of one subunit in dimeric Tai4 plays a major role in binding of Tae4, whereas a protruding loop (L4) in the other subunit is mainly responsible for inhibiting Tae4 activity. The inhibition process requires collaboration between the Tai4 dimer. These results reveal a novel and unique inhibition mechanism in effector-immunity pairs and suggest a new strategy to develop antipathogen drugs.
Collapse
Affiliation(s)
- Heng Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Structural insight into how Pseudomonas aeruginosa peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function. Biochem J 2012; 448:201-11. [DOI: 10.1042/bj20120668] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tse1 (Tse is type VI secretion exported), an effector protein produced by Pseudomonas aeruginosa, is an amidase that hydrolyses the γ-D-glutamyl-DAP (γ-D-glutamyl-L-meso-diaminopimelic acid) linkage of the peptide bridge of peptidoglycan. P. aeruginosa injects Tse1 into the periplasm of recipient cells, degrading their peptidoglycan, thereby helping itself to compete with other bacteria. Meanwhile, to protect itself from injury by Tse1, P. aeruginosa expresses the cognate immunity protein Tsi1 (Tsi is type VI secretion immunity) in its own periplasm to inactivate Tse1. In the present paper, we report the crystal structures of Tse1 and the Tse1-(6–148)–Tsi1-(20-end) complex at 1.4 Å and 1.6 Å (1 Å=0.1 nm) resolutions respectively. The Tse1 structure adopts a classical papain-like α+β fold. A cysteine–histidine catalytic diad is identified in the reaction centre of Tse1 by structural comparison and mutagenesis studies. Tsi1 binds Tse1 tightly. The HI loop (middle finger tip) from Tsi1 inserts into the large pocket of the Y-shaped groove on the surface of Tse1, and CD, EF, JK and LM loops (thumb, index finger, ring finger and little finger tips) interact with Tse1, thus blocking the binding of enzyme to peptidoglycan. The catalytic and inhibition mechanisms provide new insights into how P. aeruginosa competes with others and protects itself.
Collapse
|
42
|
Arai R, Fukui S, Kobayashi N, Sekiguchi J. Solution structure of IseA, an inhibitor protein of DL-endopeptidases from Bacillus subtilis, reveals a novel fold with a characteristic inhibitory loop. J Biol Chem 2012; 287:44736-48. [PMID: 23091053 DOI: 10.1074/jbc.m112.414763] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Bacillus subtilis, LytE, LytF, CwlS, and CwlO are vegetative autolysins, DL-endopeptidases in the NlpC/P60 family, and play essential roles in cell growth and separation. IseA (YoeB) is a proteinaceous inhibitor against the DL-endopeptidases, peptidoglycan hydrolases. Overexpression of IseA caused significantly long chained cell morphology, because IseA inhibits the cell separation DL-endopeptidases post-translationally. Here, we report the first three-dimensional structure of IseA, determined by NMR spectroscopy. The structure includes a single domain consisting of three α-helices, one 3(10)-helix, and eight β-strands, which is a novel fold like a "hacksaw." Noteworthy is a dynamic loop between β4 and the 3(10)-helix, which resembles a "blade." The electrostatic potential distribution shows that most of the surface is positively charged, but the region around the loop is negatively charged. In contrast, the LytF active-site cleft is expected to be positively charged. NMR chemical shift perturbation of IseA interacting with LytF indicated that potential interaction sites are located around the loop. Furthermore, the IseA mutants D100K/D102K and G99P/G101P at the loop showed dramatic loss of inhibition activity against LytF, compared with wild-type IseA, indicating that the β4-3(10) loop plays an important role in inhibition. Moreover, we built a complex structure model of IseA-LytF by docking simulation, suggesting that the β4-3(10) loop of IseA gets stuck deep in the cleft of LytF, and the active site is occluded. These results suggest a novel inhibition mechanism of the hacksaw-like structure, which is different from known inhibitor proteins, through interactions around the characteristic loop regions with the active-site cleft of enzymes.
Collapse
Affiliation(s)
- Ryoichi Arai
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan.
| | | | | | | |
Collapse
|
43
|
Rolain T, Bernard E, Courtin P, Bron PA, Kleerebezem M, Chapot-Chartier MP, Hols P. Identification of key peptidoglycan hydrolases for morphogenesis, autolysis, and peptidoglycan composition of Lactobacillus plantarum WCFS1. Microb Cell Fact 2012; 11:137. [PMID: 23066986 PMCID: PMC3533731 DOI: 10.1186/1475-2859-11-137] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lactobacillus plantarum is commonly used in industrial fermentation processes. Selected strains are also marketed as probiotics for their health beneficial effects. Although the functional role of peptidoglycan-degrading enzymes is increasingly documented to be important for a range of bacterial processes and host-microbe interactions, little is known about their functional roles in lactobacilli. This knowledge holds important potential for developing more robust strains resistant to autolysis under stress conditions as well as peptidoglycan engineering for a better understanding of the contribution of released muramyl-peptides as probiotic immunomodulators. RESULTS Here, we explored the functional role of the predicted peptidoglycan hydrolase (PGH) complement encoded in the genome of L. plantarum by systematic gene deletion. From twelve predicted PGH-encoding genes, nine could be individually inactivated and their corresponding mutant strains were characterized regarding their cell morphology, growth, and autolysis under various conditions. From this analysis, we identified two PGHs, the predicted N-acetylglucosaminidase Acm2 and NplC/P60 D,L-endopeptidase LytA, as key determinants in the morphology of L. plantarum. Acm2 was demonstrated to be required for the ultimate step of cell separation of daughter cells, whereas LytA appeared to be required for cell shape maintenance and cell-wall integrity. We also showed by autolysis experiments that both PGHs are involved in the global autolytic process with a dominant role for Acm2 in all tested conditions, identifying Acm2 as the major autolysin of L. plantarum WCFS1. In addition, Acm2 and the putative N-acetylmuramidase Lys2 were shown to play redundant roles in both cell separation and autolysis under stress conditions. Finally, the analysis of the peptidoglycan composition of Acm2- and LytA-deficient derivatives revealed their potential hydrolytic activities by the disappearance of specific cleavage products. CONCLUSION In this study, we showed that two PGHs of L. plantarum have a predominant physiological role in a range of growth conditions. We demonstrate that the N-acetylglucosaminidase Acm2 is the major autolysin whereas the D,L-endopeptidase LytA is a key morphogenic determinant. In addition, both PGHs have a direct impact on PG structure by generating a higher diversity of cleavage products that could be of importance for interaction with the innate immune system.
Collapse
Affiliation(s)
- Thomas Rolain
- Biochimie et Génétique Moléculaire Bactérienne, Institut des Sciences de la Vie, Université catholique de Louvain, Place Croix du Sud 5/L7,07,06, Louvain-la-Neuve, B-1348, Belgium
| | | | | | | | | | | | | |
Collapse
|
44
|
Pang XY, Cao J, Addington L, Lovell S, Battaile KP, Zhang N, Rao JLUM, Dennis EA, Moise AR. Structure/function relationships of adipose phospholipase A2 containing a cys-his-his catalytic triad. J Biol Chem 2012; 287:35260-35274. [PMID: 22923616 DOI: 10.1074/jbc.m112.398859] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Adipose phospholipase A(2) (AdPLA or Group XVI PLA(2)) plays an important role in the onset of obesity by suppressing adipose tissue lipolysis. As a consequence, AdPLA-deficient mice are resistant to obesity induced by a high fat diet or leptin deficiency. It has been proposed that AdPLA mediates its antilipolytic effects by catalyzing the release of arachidonic acid. Based on sequence homology, AdPLA is part of a small family of acyltransferases and phospholipases related to lecithin:retinol acyltransferase (LRAT). To better understand the enzymatic mechanism of AdPLA and LRAT-related proteins, we solved the crystal structure of AdPLA. Our model indicates that AdPLA bears structural similarity to proteins from the NlpC/P60 family of cysteine proteases, having its secondary structure elements configured in a circular permutation of the classic papain fold. Using both structural and biochemical evidence, we demonstrate that the enzymatic activity of AdPLA is mediated by a distinctive Cys-His-His catalytic triad and that the C-terminal transmembrane domain of AdPLA is required for the interfacial catalysis. Analysis of the enzymatic activity of AdPLA toward synthetic and natural substrates indicates that AdPLA displays PLA(1) in addition to PLA(2) activity. Thus, our results provide insight into the enzymatic mechanism and biochemical properties of AdPLA and LRAT-related proteins and lead us to propose an alternate mechanism for AdPLA in promoting adipose tissue lipolysis that is not contingent on the release of arachidonic acid and that is compatible with its combined PLA(1)/A(2) activity.
Collapse
Affiliation(s)
- Xiao-Yan Pang
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas 66045
| | - Jian Cao
- Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California San Diego, La Jolla, California 92093
| | - Linsee Addington
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas 66045
| | - Scott Lovell
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047
| | - Kevin P Battaile
- Industrial Macromolecular Crystallography Association Collaborative Access Team (IMCA-CAT), Hauptman-Woodward Medical Research Institute, Argonne, Illinois 60439
| | - Na Zhang
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047
| | - J L Uma Maheswar Rao
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas 66045
| | - Edward A Dennis
- Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California San Diego, La Jolla, California 92093
| | - Alexander R Moise
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas 66045.
| |
Collapse
|
45
|
Benz J, Sendlmeier C, Barends TRM, Meinhart A. Structural insights into the effector-immunity system Tse1/Tsi1 from Pseudomonas aeruginosa. PLoS One 2012; 7:e40453. [PMID: 22792331 PMCID: PMC3391265 DOI: 10.1371/journal.pone.0040453] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 06/07/2012] [Indexed: 11/19/2022] Open
Abstract
During an interbacterial battle, the type-6-secretion-system (T6SS) of the human pathogen Pseudomonas aeruginosa injects the peptidoglycan(PG)-hydrolase Tse1 into the periplasm of gram-negative enemy cells and induces their lysis. However, for its own benefit, P. aeruginosa produces and transports the immunity-protein Tsi1 into its own periplasm where in prevents accidental exo- and endogenous intoxication. Here we present the high-resolution X-ray crystal structure of the lytic enzyme Tse1 and describe the mechanism by which Tse1 cleaves the γ-D-glutamyl-l-meso-diaminopimelic acid amide bond of crosslinked PG. Tse1 belongs to the superfamily of N1pC/P60 peptidases but is unique among described members of this family of which the structure was described, since it is a single domain protein without any putative localization domain. Most importantly, we present the crystal structure of Tse1 bound to its immunity-protein Tsi1 as well and describe the mechanism of enzyme inhibition. Tsi1 occludes the active site of Tse1 and abolishes its enzyme activity by forming a hydrogen bond to a catalytically important histidine residue in Tse1. Based on our structural findings in combination with a bioinfomatic approach we also identified a related system in Burkholderia phytofirmans. Not only do our findings point to a common catalytic mechanism of the Tse1 PG-hydrolases, but we can also show that it is distinct from other members of this superfamily. Furthermore, we provide strong evidence that the mechanism of enzyme inhibition between Tsi1 orthologues is conserved. This work is the first structural description of an entire effector/immunity pair injected by the T6SS system. Moreover, it is also the first example of a member of the N1pC/P60 superfamily which becomes inhibited upon binding to its cognate immunity protein.
Collapse
Affiliation(s)
- Juliane Benz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Christina Sendlmeier
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| |
Collapse
|
46
|
Zhang H, Gao ZQ, Su XD, Dong YH. Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa. FEBS Lett 2012; 586:3193-9. [DOI: 10.1016/j.febslet.2012.06.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 05/30/2012] [Accepted: 06/20/2012] [Indexed: 11/27/2022]
|
47
|
Ding J, Wang W, Feng H, Zhang Y, Wang DC. Structural insights into the Pseudomonas aeruginosa type VI virulence effector Tse1 bacteriolysis and self-protection mechanisms. J Biol Chem 2012; 287:26911-20. [PMID: 22700987 DOI: 10.1074/jbc.m112.368043] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, it was identified that Pseudomonas aeruginosa competes with rival cells to gain a growth advantage using a novel mechanism that includes two interrelated processes as follows: employing type VI secretion system (T6SS) virulence effectors to lyse other bacteria, and at the same time producing specialized immunity proteins to inactivate their cognate effectors for self-protection against mutual toxicity. To explore the structural basis of these processes in the context of functional performance, the crystal structures of the T6SS virulence effector Tse1 and its complex with the corresponding immunity protein Tsi1 were determined, which, in association with mutagenesis and Biacore analyses, provided a molecular platform to resolve the relevant structural questions. The results indicated that Tse1 features a papain-like structure and conserved catalytic site with distinct substrate-binding sites to hydrolyze its murein peptide substrate. The immunity protein Tsi1 interacts with Tse1 via a unique interactive recognition mode to shield Tse1 from its physiological substrate. These findings reveal both the structural mechanisms for bacteriolysis and the self-protection against the T6SS effector Tse1. These mechanisms are significant not only by contributing to a novel understanding of niche competition among bacteria but also in providing a structural basis for antibacterial agent design and the development of new strategies to fight P. aeruginosa.
Collapse
Affiliation(s)
- Jingjin Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 10010, China
| | | | | | | | | |
Collapse
|
48
|
Chou S, Bui NK, Russell AB, Lexa KW, Gardiner TE, LeRoux M, Vollmer W, Mougous JD. Structure of a peptidoglycan amidase effector targeted to Gram-negative bacteria by the type VI secretion system. Cell Rep 2012; 1:656-64. [PMID: 22813741 DOI: 10.1016/j.celrep.2012.05.016] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 05/11/2012] [Accepted: 05/21/2012] [Indexed: 12/21/2022] Open
Abstract
The target range of a bacterial secretion system can be defined by effector substrate specificity or by the efficacy of effector delivery. Here, we report the crystal structure of Tse1, a type VI secretion (T6S) bacteriolytic amidase effector from Pseudomonas aeruginosa. Consistent with its role as a toxin, Tse1 has a more accessible active site than related housekeeping enzymes. The activity of Tse1 against isolated peptidoglycan shows its capacity to act broadly against Gram-negative bacteria and even certain Gram-positive species. Studies with intact cells indicate that Gram-positive bacteria can remain vulnerable to Tse1 despite cell wall modifications. However, interbacterial competition studies demonstrate that Tse1-dependent lysis is restricted to Gram-negative targets. We propose that the previously observed specificity for T6S against Gram-negative bacteria is a consequence of high local effector concentration achieved by T6S-dependent targeting to its site of action rather than inherent effector substrate specificity.
Collapse
Affiliation(s)
- Seemay Chou
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Coggill P, Bateman A. The YARHG domain: an extracellular domain in search of a function. PLoS One 2012; 7:e35575. [PMID: 22615736 PMCID: PMC3355149 DOI: 10.1371/journal.pone.0035575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 03/19/2012] [Indexed: 11/30/2022] Open
Abstract
We have identified a new bacterial protein domain that we hypothesise binds to peptidoglycan. This domain is called the YARHG domain after the most highly conserved sequence-segment. The domain is found in the extracellular space and is likely to be composed of four alpha-helices. The domain is found associated with protein kinase domains, suggesting it is associated with signalling in some bacteria. The domain is also found associated with three different families of peptidases. The large number of different domains that are found associated with YARHG suggests that it is a useful functional module that nature has recombined multiple times.
Collapse
Affiliation(s)
- Penny Coggill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
| | | |
Collapse
|
50
|
Böth D, Schneider G, Schnell R. Peptidoglycan Remodeling in Mycobacterium tuberculosis: Comparison of Structures and Catalytic Activities of RipA and RipB. J Mol Biol 2011; 413:247-60. [DOI: 10.1016/j.jmb.2011.08.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/02/2011] [Accepted: 08/06/2011] [Indexed: 11/26/2022]
|