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The British Journal of Nutrition Sep 2021Muramidases constitute a superfamily of enzymes that hydrolyse peptidoglycan (PGN) from bacterial cell walls. Recently, a fungal muramidase derived from Acremonium...
Muramidases constitute a superfamily of enzymes that hydrolyse peptidoglycan (PGN) from bacterial cell walls. Recently, a fungal muramidase derived from Acremonium alcalophilum has been shown to increase broiler performance when added as a feed additive. However, the underlying mechanisms of action are not yet identified. Here, we investigated the hypothesis that this muramidase can cleave PGN to muramyl dipeptide (MDP), activating nucleotide-binding oligomerisation domain-containing protein 2 (NOD2) receptors in eukaryotic cells, potentially inducing anti-inflammatory host responses. Using Micrococcus luteus as a test bacterium, it was shown that muramidase from A. alcalophilum did not display antimicrobial activity, while it could cleave fluorescently labelled PGN. It was shown that the muramidase could degrade PGN down to its minimal bioactive structure MDP by using UPLC-MS/MS. Using HEK-Blue™-hNOD2 reporter cells, it was shown that the muramidase-treated PGN degradation mixture could activate NOD2. Muramidase supplementation to broiler feed increased the duodenal goblet cell and intraepithelial lymphocyte abundance while reducing duodenal wall CD3+ T lymphocyte levels. Muramidase supplementation to broiler feed only had moderate effects on the duodenal, ileal and caecal microbiome. It was shown that the newly discovered muramidase hydrolysed PGN, resulting in MDP that activates NOD2, potentially steering the host response for improved intestinal health.
Topics: Acetylmuramyl-Alanyl-Isoglutamine; Animal Nutritional Physiological Phenomena; Animals; Bacteria; Cell Wall; Cells, Cultured; Chickens; Chromatography, Liquid; Duodenum; Inflammation; Muramidase; Nod2 Signaling Adaptor Protein; Peptidoglycan; Tandem Mass Spectrometry
PubMed: 33172510
DOI: 10.1017/S0007114520004493 -
Nucleic Acids Research Jul 2017Antibodies have become an indispensable tool for many biotechnological and clinical applications. They bind their molecular target (antigen) by recognizing a portion of...
Antibodies have become an indispensable tool for many biotechnological and clinical applications. They bind their molecular target (antigen) by recognizing a portion of its structure (epitope) in a highly specific manner. The ability to predict epitopes from antigen sequences alone is a complex task. Despite substantial effort, limited advancement has been achieved over the last decade in the accuracy of epitope prediction methods, especially for those that rely on the sequence of the antigen only. Here, we present BepiPred-2.0 (http://www.cbs.dtu.dk/services/BepiPred/), a web server for predicting B-cell epitopes from antigen sequences. BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures. This new method was found to outperform other available tools for sequence-based epitope prediction both on epitope data derived from solved 3D structures, and on a large collection of linear epitopes downloaded from the IEDB database. The method displays results in a user-friendly and informative way, both for computer-savvy and non-expert users. We believe that BepiPred-2.0 will be a valuable tool for the bioinformatics and immunology community.
Topics: Epitopes, B-Lymphocyte; Internet; Models, Molecular; Muramidase; Protein Conformation; Sequence Analysis, Protein; Software; User-Computer Interface
PubMed: 28472356
DOI: 10.1093/nar/gkx346 -
EXS 1996Bacteriophage genomes encode lysozymes whose role is to favour the release of virions by lysis of the host cells or to facilitate infection. In this review, the... (Review)
Review
Bacteriophage genomes encode lysozymes whose role is to favour the release of virions by lysis of the host cells or to facilitate infection. In this review, the evolutionary relationships between the phage lysozymes are described. They are grouped into several classes: the V-, the G-, the lambda- and the CH-type lysozymes. The results of structure determinations and of enzymological studies indicate that the enzymes belonging to the first two classes, and possibly the third, share common structural elements with C-type lysozymes (eg. hen egg white lysozyme). The proteins of the fourth class, on the other hand, are structurally similar to the S. erythraeus lysozyme. Several phage lysozymes feature a modular construction: besides the catalytic domain, they contain additional domains or repeated motifs presumed to be important for binding to the bacterial walls and for efficient catalysis. The mechanism of action of these enzymes is described and the role of the important amino acid residues is discussed on the basis of sequence comparisons and of mutational studies. The effects of mutations affecting the structure and of multiple mutations are also discussed, particularly in the case of the T4 lysozyme: from these studies, proteins appear to be quite tolerant of potentially disturbing modifications.
Topics: Amino Acid Sequence; Bacteria; Bacteriophages; Carbohydrate Sequence; Cell Wall; Evolution, Molecular; Molecular Sequence Data; Muramidase; Mutagenesis; Protein Conformation; Protein Structure, Secondary; Sequence Alignment; Substrate Specificity
PubMed: 8765293
DOI: 10.1007/978-3-0348-9225-4_3 -
Journal of Bacteriology Nov 2007We have characterized open reading frame RSP0072, which is located within the flgG operon in Rhodobacter sphaeroides. The amino acid sequence analysis of this gene...
We have characterized open reading frame RSP0072, which is located within the flgG operon in Rhodobacter sphaeroides. The amino acid sequence analysis of this gene product showed the presence of a soluble lytic transglycosylase domain. The deletion of the N-terminal region (90 amino acids) of the product of RSP0072 yields a leaky nonmotile phenotype, as determined by swarm assays in soft agar. Electron micrographs revealed the lack of flagella in mutant cells. The purified wild-type protein showed lytic activity on extracts of Micrococcus luteus. In contrast, no lytic activity was observed when the residues E57 or E83 were replaced by alanine. Affinity blotting suggests that the protein encoded by RSP0072 interacts with the flagellar rod-scaffolding protein FlgJ, which lacks the muramidase domain present in FlgJ of many bacteria. We propose that the product of RSP0072 is a flagellar muramidase that is exported to the periplasm via the Sec pathway, where it interacts with FlgJ to open a gap in the peptidoglycan layer for the subsequent penetration of the nascent flagellar structure.
Topics: Flagella; Gene Expression Regulation, Bacterial; Muramidase; Mutation; Open Reading Frames; Operon; Photosynthesis; Protein Binding; Rhodobacter sphaeroides
PubMed: 17873041
DOI: 10.1128/JB.01073-07 -
Trends in Microbiology Oct 2005Bacteriophage lytic enzymes, or lysins, are highly evolved molecules produced by bacterial viruses (bacteriophage) to digest the bacterial cell wall for bacteriophage... (Review)
Review
Bacteriophage lytic enzymes, or lysins, are highly evolved molecules produced by bacterial viruses (bacteriophage) to digest the bacterial cell wall for bacteriophage progeny release. Small quantities of purified recombinant lysin added to gram-positive bacteria causes immediate lysis resulting in log-fold death of the target bacterium. Lysins have now been used successfully in animal models to control pathogenic antibiotic resistant bacteria found on mucosal surfaces and in blood. The advantages over antibiotics are their specificity for the pathogen without disturbing the normal flora, the low chance of bacterial resistance to lysins and their ability to kill colonizing pathogens on mucosal surfaces, capabilities that were previously unavailable. Thus, lysins could be an effective anti-infective in an age of mounting antibiotic resistance.
Topics: Amidohydrolases; Anti-Bacterial Agents; Bacteria; Bacteriophages; Endopeptidases; Muramidase; Substrate Specificity
PubMed: 16125935
DOI: 10.1016/j.tim.2005.08.007 -
Postepy Higieny I Medycyny... Dec 2014Lysozyme (LZ, muramidase, N-acetylmuramylhydrolase) is a protein occuring in animals, plants, bacteria and viruses. It can be found e.g. in granules of neutrophils,... (Review)
Review
Lysozyme (LZ, muramidase, N-acetylmuramylhydrolase) is a protein occuring in animals, plants, bacteria and viruses. It can be found e.g. in granules of neutrophils, macrophages and in serum, saliva, milk, honey and hen egg white. The enzyme hydrolyzes the β-1,4 glycosidic bonds between N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) of cell wall peptidoglycan (PG) in Gram-positive and Gram-negative bacteria. In the animal kingdom, three muramidase types have been identified: the c-type (chicken type), the g-type (goose-type) and the i-type (invertebrates). The c-type LZ from hen egg white is a model for the study of protein structure and function. Muramidase shows bactericidal activity mainly against Gram-positive bacteria. Cytolytic activity against cells of Gram-negative bacteria has not been proved. Bacterial cells have developed defense mechanisms that allow them to avoid the action of LZ. They are based e.g. on the production of enzyme inhibitors or modification of the PG. LZ is one of the most studied enzymes and yet not all aspects characterizing this protein are fully understood. One of the most important unresolved issues concerning the biological function of LZ is the role of muramidase in the bactericidal action of serum against Gram-negative bacteria. In order to clarify the function of LZ, the enzyme is e.g. removed from the serum by adsorption onto bentonite (montmorillonite, MMT). By using X-ray diffraction techniques it has been shown that MMT after contact with the serum is delaminated. The problems associated with folding of muramidase and LZ participation in the development of amyloidoses also await explanation.
Topics: Animals; Anti-Bacterial Agents; Gram-Negative Bacteria; Gram-Positive Bacteria; Muramidase
PubMed: 25531714
DOI: 10.5604/17322693.1133100 -
Food Chemistry Feb 2019Lysozyme, an important bacteriostatic protein, is widely distributed in nature. It is generally believed that the high efficiency of lysozyme in inhibiting gram-positive... (Review)
Review
Lysozyme, an important bacteriostatic protein, is widely distributed in nature. It is generally believed that the high efficiency of lysozyme in inhibiting gram-positive bacteria is caused by its ability to cleave the β-(1,4)-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine. In recent years, there has been growing interest in modifying lysozyme via physical or chemical interactions in order to improve its sensitivity against gram-negative bacterial strains. This review addresses some significant techniques, including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), infrared (IR) spectra, fluorescence spectroscopy, nuclear magnetic resonance (NMR), UV-vis spectroscopy, circular dichroism (CD) spectra and differential scanning calorimetry (DSC), which can be used to characterize lysozymes and methods that modify lysozymes with carbohydrates to enhance their various physicochemical characteristics. The applications of biomaterials based on lysozymes in different food matrices are also discussed.
Topics: Food Industry; Gram-Negative Bacteria; Gram-Positive Bacteria; Immobilized Proteins; Maillard Reaction; Muramidase; Static Electricity
PubMed: 30372997
DOI: 10.1016/j.foodchem.2018.09.017 -
Protein Science : a Publication of the... Apr 2010An overview is presented of some of the major insights that have come from studies of the structure, stability, and folding of T4 phage lysozyme. A major purpose of this... (Review)
Review
An overview is presented of some of the major insights that have come from studies of the structure, stability, and folding of T4 phage lysozyme. A major purpose of this review is to provide the reader with a complete tabulation of all of the variants that have been characterized, including melting temperatures, crystallographic data, Protein Data Bank access codes, and references to the original literature. The greatest increase in melting temperature (T(m)) for any point mutant is 5.1 degrees C for the mutant Ser 117 --> Val. This is achieved in part not only by hydrophobic stabilization but also by eliminating an unusually short hydrogen bond of 2.48 A that apparently has an unfavorable van der Waals contact. Increases in T(m) of more than 3-4 degrees C for point mutants are rare, whereas several different types of destabilizing substitutions decrease T(m) by 20 degrees C or thereabouts. The energetic cost of cavity creation and its relation to the hydrophobic effect, derived from early studies of "large-to-small" mutants in the core of T4 lysozyme, has recently been strongly supported by related studies of the intrinsic membrane protein bacteriorhodopsin. The L99A cavity in the C-terminal domain of the protein, which readily binds benzene and many other ligands, has been the subject of extensive study. Crystallographic evidence, together with recent NMR analysis, suggest that these ligands are admitted by a conformational change involving Helix F and its neighbors. A total of 43 nonisomorphous crystal forms of different monomeric lysozyme mutants were obtained plus three more for synthetically-engineered dimers. Among the 43 space groups, P2(1)2(1)2(1) and P2(1) were observed most frequently, consistent with the prediction of Wukovitz and Yeates.
Topics: Animals; Bacteriophage T4; Binding Sites; Crystallography, X-Ray; Humans; Models, Molecular; Muramidase; Mutation; Protein Conformation; Protein Folding; Structure-Activity Relationship; Thermodynamics
PubMed: 20095051
DOI: 10.1002/pro.344 -
Critical Reviews in Biotechnology Dec 2016Lysozyme is an antimicrobial peptide with a high enzymatic activity and positive charges. Therefore, it has applications in food and pharmaceutical industries as an... (Review)
Review
Lysozyme is an antimicrobial peptide with a high enzymatic activity and positive charges. Therefore, it has applications in food and pharmaceutical industries as an antimicrobial agent. Lysozyme is ubiquitous in both animal and plant kingdoms. Currently, egg-white lysozyme is the most commercially available form of lysozyme. The main concerns of egg-white lysozyme are high recovery cost, low activity and most importantly the immunological problems to some people. Therefore, human lysozyme production has gained importance in recent years. Scientists have developed transgenic plants, animals and microorganisms that can produce human lysozyme. Out of these, microbial production has advantages for commercial productions, because high production levels are achievable in a relatively short time. It has been reported that fermentation parameters, such as pH, temperature, aeration, are key factors to increase the effectiveness of the human lysozyme production. Moreover, purification of the lysozyme from the fermentation broth needs to be optimized for the economical production. In conclusion, this review paper covers the mechanism of lysozyme, its sources, production methods and recovery of lysozyme.
Topics: Animals; Anti-Infective Agents; Bacteria; Humans; Muramidase
PubMed: 26383819
DOI: 10.3109/07388551.2015.1084263 -
Nordisk Medicin Mar 1971
Review
Topics: Animals; Blood Cells; Dogs; Graft Rejection; Humans; Iodine Isotopes; Kidney Diseases; Kidney Transplantation; Leukemia; Muramidase; Rats
PubMed: 4928570
DOI: No ID Found