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Bioorganic & Medicinal Chemistry Letters May 2019The innate immune system is the body's first defense against invading microorganisms, relying on the recognition of bacterial-derived small molecules by host protein... (Review)
Review
The innate immune system is the body's first defense against invading microorganisms, relying on the recognition of bacterial-derived small molecules by host protein receptors. This recognition event and downstream immune response rely heavily on the specific chemical features of both the innate immune receptors and their bacterial derived ligands. This review presents a chemist's perspective on some of the most crucial and complex components of two receptors (NOD1 and NOD2): starting from the structural and chemical characteristics of bacterial-derived small molecules, to the specific proposed models of molecular recognition of these molecules by immune receptors, to the subsequent post-translational modifications that ultimately dictate downstream immune signaling. Recent advances in the field are discussed, as well as the potential for the development of targeted therapeutics.
Topics: Bacteria; Humans; Immunity, Innate; Nod1 Signaling Adaptor Protein; Nod2 Signaling Adaptor Protein; Peptidoglycan; Protein Processing, Post-Translational; Signal Transduction
PubMed: 30890292
DOI: 10.1016/j.bmcl.2019.03.010 -
Critical Reviews in Biochemistry and... Oct 2017The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are... (Review)
Review
The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores. Significant advances in the mechanistic understanding of each of these processes have coincided with the successive discovery of new LTs structures. In this review, we provide a systematic perspective on what is known on the structure-function correlations for the LTs, while simultaneously identifying numerous opportunities for the future study of these enigmatic enzymes.
Topics: Bacteria; Bacterial Proteins; Cell Wall; Glycosyltransferases; Peptidoglycan
PubMed: 28644060
DOI: 10.1080/10409238.2017.1337705 -
Molecular Microbiology May 2013Decades of study have revealed the fine chemical structure of the bacterial peptidoglycan cell wall, but the arrangement of the peptidoglycan strands within the wall has...
Decades of study have revealed the fine chemical structure of the bacterial peptidoglycan cell wall, but the arrangement of the peptidoglycan strands within the wall has been challenging to define. The application of electron cryotomography (ECT) and new methods for fluorescent labelling of peptidoglycan are allowing new insights into wall structure and synthesis. Two articles in this issue examine peptidoglycan structures in the model Gram-positive species Bacillus subtilis. Beeby et al. combined visualization of peptidoglycan using ECT with molecular modelling of three proposed arrangements of peptidoglycan strands to identify the model most consistent with their data. They argue convincingly for a Gram-positive wall containing multiple layers of peptidoglycan strands arranged circumferentially around the long axis of the rod-shaped cell, an arrangement similar to the single layer of peptidoglycan in similarly shaped Gram-negative cells. Tocheva et al. examined sporulating cells using ECT and fluorescence microscopy to demonstrate the continuous production of a thin layer of peptidoglycan around the developing spore as it is engulfed by the membrane of the adjacent mother cell. The presence of this peptidoglycan in the intermembrane space allows the refinement of a model for engulfment, which has been known to include peptidoglycan synthetic and lytic functions.
Topics: Bacillus subtilis; Cell Wall; Peptidoglycan; Spores, Bacterial
PubMed: 23551458
DOI: 10.1111/mmi.12212 -
Plant Physiology Aug 2022Accumulating evidence suggests that peptidoglycan, consistent with a bacterial cell wall, is synthesized around the chloroplasts of many photosynthetic eukaryotes, from...
Accumulating evidence suggests that peptidoglycan, consistent with a bacterial cell wall, is synthesized around the chloroplasts of many photosynthetic eukaryotes, from glaucophyte algae to early-diverging land plants including pteridophyte ferns, but the biosynthetic pathway has not been demonstrated. Here, we employed mass spectrometry and enzymology in a two-fold approach to characterize the synthesis of peptidoglycan in chloroplasts of the moss Physcomitrium (Physcomitrella) patens. To drive the accumulation of peptidoglycan pathway intermediates, P. patens was cultured with the antibiotics fosfomycin, D-cycloserine, and carbenicillin, which inhibit key peptidoglycan pathway proteins in bacteria. Mass spectrometry of the trichloroacetic acid-extracted moss metabolome revealed elevated levels of five of the predicted intermediates from uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) through the uridine diphosphate N-acetylmuramic acid (UDP-MurNAc)-D,L-diaminopimelate (DAP)-pentapeptide. Most Gram-negative bacteria, including cyanobacteria, incorporate meso-diaminopimelic acid (D,L-DAP) into the third residue of the stem peptide of peptidoglycan, as opposed to L-lysine, typical of most Gram-positive bacteria. To establish the specificity of D,L-DAP incorporation into the P. patens precursors, we analyzed the recombinant protein UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase (MurE) from both P. patens and the cyanobacterium Anabaena sp. (Nostoc sp. strain PCC 7120). Both ligases incorporated D,L-DAP in almost complete preference to L-Lys, consistent with the mass spectrophotometric data, with catalytic efficiencies similar to previously documented Gram-negative bacterial MurE ligases. We discuss how these data accord with the conservation of active site residues common to DL-DAP-incorporating bacterial MurE ligases and of the probability of a horizontal gene transfer event within the plant peptidoglycan pathway.
Topics: Bacteria; Cell Wall; Chloroplasts; Gram-Negative Bacteria; Ligases; Lysine; Peptidoglycan; Uridine Diphosphate
PubMed: 35471580
DOI: 10.1093/plphys/kiac176 -
Journal of Industrial Microbiology &... Apr 2021This study evaluates peptidoglycan hydrolysis by a microbial muramidase from the fungus Acremonium alcalophilum in vitro and in the gastrointestinal tract of broiler...
This study evaluates peptidoglycan hydrolysis by a microbial muramidase from the fungus Acremonium alcalophilum in vitro and in the gastrointestinal tract of broiler chickens. Peptidoglycan used for in vitro studies was derived from 5 gram-positive chicken gut isolate type strains. In vitro peptidoglycan hydrolysis was studied by three approaches: (a) helium ion microscopy to identify visual phenotypes of hydrolysis, (b) reducing end assay to quantify solubilization of peptidoglycan fragments, and (c) mass spectroscopy to estimate relative abundances of soluble substrates and reaction products. Visual effects of peptidoglycan hydrolysis could be observed by helium ion microscopy and the increase in abundance of soluble peptidoglycan due to hydrolysis was quantified by a reducing end assay. Mass spectroscopy confirmed the release of hydrolysis products and identified muropeptides from the five different peptidoglycan sources. Peptidoglycan hydrolysis in chicken crop, jejunum, and caecum samples was measured by quantifying the total and soluble muramic acid content. A significant increase in the proportion of the soluble muramic acid was observed in all three segments upon inclusion of the microbial muramidase in the diet.
Topics: Acremonium; Animals; Chickens; Gastrointestinal Tract; Hydrolysis; Male; Muramidase; Peptidoglycan
PubMed: 33693885
DOI: 10.1093/jimb/kuab008 -
Journal of the American Chemical Society Aug 2019The bacterial cell wall is composed of peptidoglycan, and its biosynthesis is an established target for antibiotics. Peptidoglycan is assembled from a glycopeptide...
The bacterial cell wall is composed of peptidoglycan, and its biosynthesis is an established target for antibiotics. Peptidoglycan is assembled from a glycopeptide precursor, Lipid II, that is polymerized by peptidoglycan glycosyltransferases into glycan strands that are subsequently cross-linked to form the mature cell wall. For decades bacteria were thought to contain only one family of enzymes that polymerize Lipid II, but recently, the ubiquitous Shape, Elongation, Division, and Sporulation (SEDS)-family proteins RodA and FtsW were shown to be peptidoglycan polymerases. Because RodA and FtsW are essential in nearly all bacteria, these enzymes are promising targets for new antibiotics. However, almost nothing is known about the mechanisms of these polymerases. Here, we report that SEDS proteins synthesize peptidoglycan by adding new Lipid II monomers to the reducing end of the growing glycan chain. Using substrates that can only react at the reducing end, we also show that the glycosyl donor and acceptor in the polymerization reaction have distinct lipid requirements. These findings provide the first fundamental insights into the mechanism of SEDS-family polymerases and lay the groundwork for future biochemical and structural studies.
Topics: Bacterial Proteins; Biosynthetic Pathways; Humans; Peptidoglycan; Peptidoglycan Glycosyltransferase; Staphylococcal Infections; Staphylococcus aureus; Substrate Specificity
PubMed: 31386359
DOI: 10.1021/jacs.9b06358 -
Cellular and Molecular Life Sciences :... Sep 2003The innate immune system recognizes microorganisms through a series of pattern recognition receptors that are highly conserved in evolution. Peptidoglycan (PGN) is a... (Review)
Review
The innate immune system recognizes microorganisms through a series of pattern recognition receptors that are highly conserved in evolution. Peptidoglycan (PGN) is a unique and essential component of the cell wall of virtually all bacteria and is not present in eukaryotes, and thus is an excellent target for the innate immune system. Indeed, higher eukaryotes, including mammals, have several PGN recognition molecules, including CD14, Toll-like receptor 2, a family of peptidoglycan recognition proteins, Nod1 and Nod2, and PGN-lytic enzymes (lysozyme and amidases). These molecules induce host responses to microorganisms or have direct antimicrobial effects.
Topics: Adaptor Proteins, Signal Transducing; Animals; Bacteria; Carrier Proteins; Humans; Immune System; Immunity, Innate; Lipopolysaccharide Receptors; Membrane Glycoproteins; Molecular Structure; Nod1 Signaling Adaptor Protein; Peptidoglycan; Receptors, Cell Surface; Toll-Like Receptor 2; Toll-Like Receptors
PubMed: 14523544
DOI: 10.1007/s00018-003-3019-6 -
The Journal of Biological Chemistry Mar 2019In general, the last step in the vegetative cycle of bacterial viruses, or bacteriophages, is lysis of the host. dsDNA phages require multiple lysis proteins, including... (Review)
Review
In general, the last step in the vegetative cycle of bacterial viruses, or bacteriophages, is lysis of the host. dsDNA phages require multiple lysis proteins, including at least one enzyme that degrades the cell wall (peptidoglycan (PG)). In contrast, the lytic ssDNA and ssRNA phages have a single lysis protein that achieves cell lysis without enzymatically degrading the PG. Here, we review four "single-gene lysis" or Sgl proteins. Three of the Sgls block bacterial cell wall synthesis by binding to and inhibiting several enzymes in the PG precursor pathway. The target of the fourth Sgl, L from bacteriophage MS2, is still unknown, but we review evidence indicating that it is likely a protein involved in maintaining cell wall integrity. Although only a few phage genomes are available to date, the ssRNA are a rich source of novel Sgls, which may facilitate further unraveling of bacterial cell wall biosynthesis and discovery of new antibacterial agents.
Topics: Bacteria; Bacterial Proteins; Cell Wall; Genes, Viral; Levivirus; Peptidoglycan
PubMed: 30420429
DOI: 10.1074/jbc.TM118.001773 -
Journal of Molecular Biology Feb 2012Mycobacterium tuberculosis ArfA (Rv0899) is a membrane protein encoded by an operon that is required for supporting bacterial growth in acidic environments. Its...
Mycobacterium tuberculosis ArfA (Rv0899) is a membrane protein encoded by an operon that is required for supporting bacterial growth in acidic environments. Its C-terminal domain (C domain) shares significant sequence homology with the OmpA-like family of peptidoglycan-binding domains, suggesting that its physiological function in acid stress protection may be related to its interaction with the mycobacterial cell wall. Previously, we showed that ArfA forms three independently structured modules, and we reported the structure of its central domain (B domain). Here, we describe the high-resolution structure and dynamics of the C domain, we identify ArfA as a peptidoglycan-binding protein and we elucidate the molecular basis for its specific recognition of diaminopimelate-type peptidoglycan. The C domain of ArfA adopts the characteristic fold of the OmpA-like family. It exhibits pH-dependent conformational dynamics (with significant heterogeneity at neutral pH and a more ordered structure at acidic pH), which could be related to its acid stress response. The C domain associates tightly with polymeric peptidoglycan isolated from M. tuberculosis and also associates with a soluble peptide intermediate of peptidoglycan biosynthesis. This enabled us to characterize the peptidoglycan binding site where five highly conserved ArfA residues, including two key arginines, establish the specificity for diaminopimelate- but not Lys-type peptidoglycan. ArfA is the first peptidoglycan-binding protein to be identified in M. tuberculosis. Its functions in acid stress protection and peptidoglycan binding suggest a link between the acid stress response and the physicochemical properties of the mycobacterial cell wall.
Topics: Bacterial Outer Membrane Proteins; Binding Sites; Crystallography, X-Ray; Diaminopimelic Acid; Hydrogen-Ion Concentration; Models, Molecular; Mycobacterium tuberculosis; Peptidoglycan; Protein Conformation
PubMed: 22206986
DOI: 10.1016/j.jmb.2011.12.030 -
Antimicrobial Agents and Chemotherapy Sep 2022Bacteriophages and bacteriophage-derived peptidoglycan hydrolases (endolysins) present promising alternatives for the treatment of infections caused by multidrug...
Bacteriophages and bacteriophage-derived peptidoglycan hydrolases (endolysins) present promising alternatives for the treatment of infections caused by multidrug resistant Gram-negative and Gram-positive pathogens. In this study, Gp105, a putative lysozyme murein hydrolase from Enterobacter phage myPSH1140 was characterized as well as using the purified protein. Gp105 contains a T4-type lysozyme-like domain (IPR001165) and belongs to Glycoside hydrolase family 24 (IPR002196). The putative endolysin indeed had strong antibacterial activity against Gram-negative pathogens, including E. cloacae, K. pneumoniae, P. aeruginosa, S. marcescens sp., and A. baumannii. Also, an peptidoglycan hydrolysis assay showed strong activity against purified peptidoglycans. This study demonstrates the potential of Gp105 to be used as an antibacterial protein to combat Gram-negative pathogens.
Topics: Anti-Bacterial Agents; Bacteriophages; Endopeptidases; Enterobacter; Glycoside Hydrolases; Klebsiella pneumoniae; Muramidase; Myoviridae; N-Acetylmuramoyl-L-alanine Amidase; Peptidoglycan; Pseudomonas aeruginosa
PubMed: 35950843
DOI: 10.1128/aac.00506-22