Structural basis of the binding of fatty acids to peptidoglycan recognition protein, PGRP-S through second binding site

A Review on the Extraction, Structural Characterization, Function, and Applications of Peptidoglycan

Peptidoglycan (PGN) is the primary component of bacterial cell walls, consisting of linear glycan chains formed by alternating linkages of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) through glycosidic bonds. It exhibits biological activity in various aspects, making it a biologically significant macromolecule with extensive industrial application. This review aims to explore the latest research advancements in the extraction techniques, structural characterization, functions, and applications of PGN. The review compares the advantages and limitations of traditional chemical lysis methods with modern mechanical-assisted and bio-assisted extraction techniques, discusses chemical composition analysis techniques and structural characterization methods of PGN. The review emphasizes the potential of PGN in immune modulation, specific recognition, and adsorption functions. Furthermore, the review examines potential applications of PGN in vaccine development, the livestock industry, the removal of harmful substances, and protein bioprocessing. In the end, based on the current development trend, future research directions for PGN are proposed, including in-depth studies on the mechanisms of PGN in different hosts and its immunomodulatory effects in various disease models. It is expected that a comprehensive reference framework for the research and application of PGN will be provided through this review, offering ideas and directions for further development and utilization.

Structure of the complex of camel peptidoglycan recognition protein-S with hexanoic acid reveals novel features of the versatile ligand-binding site at the dimeric interface

The short peptidoglycan recognition protein (PGRP-S) of the innate immune system recognizes the invading microbes through binding to their cell wall molecules. In order to understand the mode of binding of PGRP-S to bacterial cell wall molecules, the structure of the complex of camel PGRP-S (CPGRP-S) with hexanoic acid has been determined at 2.07 Å resolution. Previously, we had reported the structures of CPGRP-S in the native unbound state as well as in the complexed forms with the components of various bacterial cell wall molecules such as peptidoglycan (PGN), lipopolysaccharide (LPS), lipoteichoic acid (LTA), mycolic acid (MA) and other fatty acids. These structures revealed that CPGRP-S formed two homodimers which were designated as A-B and CD dimers. It also showed that the fatty acids bind to CPGRP-S in the binding site at the A-B dimer while the non-fatty acids were shown to bind at the interfaces of both A-B and CD dimers. The present structure of the complex of CPGRP-S with hexanoic acid (HA) showed that HA binds to CPGRP-S at the interface of CD dimer. HA was located in the same groove at the CD interface which was occupied by non-fatty acids such as PGN, LPS and LTA and interacts with residues from both C and D molecules. HA is firmly held in the groove with several hydrogen bonds and a number of van der Waals contacts. This is the first structure which reports the binding of a fatty acid in the cleft at the interface of CD dimer.

Peptidoglycan-based immunomodulation

Peptidoglycan (PGN) is a unique component in the cytoderm of prokaryotes which can be recognized by different pathogen-associated molecular patterns (PAMPs) in eukaryotes, followed by a cascade of immune responses via different pathways. This review outlined the basic structure of PGN, its immunologic functions. The immunomodulation pathways mediated by PGN were elaborated. PGN induces specific immunity through stimulating different cytokine release and Th1/Th2-dominated immune responses during humoral/cellular immune response. The nonspecific immunity activation by PGN involves immunomodulation by different pattern recognition receptors (PRRs) including PGN recognition proteins (PGRPs), nucleotide oligomerization domain (NOD)-like receptors (NLRs), Toll-like receptors (TLRs), and C-type lectin receptors (CLRs). The sources and classification of PGRPs were summarized. In view of the stimulating activities of PGN and its monomers, the potential application of PGN as vaccine or adjuvant was prospected. This review provides systematic information on PGN functionalities from the point of immunoregulation, which might be useful in the deep exploitation of PGN.Key points. The immunological functions of PGN were illustrated. Cellular and humoral immunomodulation by PGN were outlined. The use of PGN as vaccine or adjuvant was prospected.

Two short peptidoglycan recognition proteins from Crassostrea gigas with similar structure exhibited different PAMP binding activity

Peptidoglycan recognition protein (PGRP) is an essential molecule in innate immunity for both invertebrates and vertebrates, owing to its prominent ability in specifically recognizing bacterial peptidoglycan (PGN) and eliminating the invading bacteria. In the present study, the full length cDNA of two PGRP genes, CgPGRPS2 and CgPGRPS4, were cloned from oyster Crassostrea gigas. Their amino acid sequences both contained one signal peptide, one typical PGRP/amidase domain with conserved catalytic residues responsible for amidase activity (55H, 90Y, 164H, 172C in CgPGRPS2, and 98H, 133Y, 207H, 215C in CgPGRPS4), and specific PGN recognition (84R, 85W, 104R, 109V in CgPGRPS2, and 127G, 128W, 147R, 152V in CgPGRPS4), and they shared 55.9% sequence similarity. The mRNA transcripts of CgPGRPS2 and CgPGRPS4 were constitutively expressed in all the examined tissues, including haemocytes, hepatopancreas, mantle, gonad, heart, adductor muscle and gill, with the highest expression level in adductor muscle and hepatopancreas, respectively. Both CgPGRPS2 and CgPGRPS4 proteins were mainly localized in the cytoplasma. The recombinant protein of CgPGRPS2 (rCgPGRPS2) could bind lipopolysaccharide (LPS), PGN and mannan (Man), as well as various microorganisms including Gram-negative bacteria Escherichia coli, Vibrio anguillarum, Gram-positive bacteria Staphylococcus aureus and fungi Yarrowia lipolytica. The recombinant protein of CgPGRPS4 (rCgPGRPS4) exhibited higher binding affinity to PGN, lower binding affinity to LPS, while no binding activity to Man and Y. lipolytica. The results indicated that CgPGRPS2 and CgPGRPS4 could function as pattern recognition receptors (PRR) in the innate immune response of oyster, and they exhibited a certain degree of functional differentiation in recognition of Man.

Impact of host genetics on susceptibility and resistance to Mycobacterium avium subspecies Paratuberculosis infection in domestic ruminants

Johne's disease or Paratuberculosis has emerged as major infectious disease of animals in general and domestic livestock in particular on global basis. There have been major initiatives in developed countries for the control of this incurable malady of animals and human beings alike (inflammatory bowel disease or Crohn's disease). Disease has not received similar attention due to inherent complexities of disease, diagnosis and control, in resource poor counties around the world. However, the rich genetic diverstiy of the otherwise low productive animal population offers opportunity for the control of Johne's disease and improve per animal productivity. Present review aims to gather and compile information available on genetics or resistance to Johne's disease and its future exploitation by resource poor countries rich in animal diversity. This review will also help to create awareness and share knowledge and experience on prevalence and opportunities for control of Johne's disease in the livestock population to boost per animal productivity among developing and poor countries of the world. Breeding of animals for disease resistance provides good, safe, effective and cheaper way of controlling Johne's disease in animals, with especial reference to domestic livestock of developing and poor countries. Study will help to establish better understanding of the correlation between host cell factors and resistance to MAP infection which may have ultimately help in the control of Johne's disease in future.

Structural insights into the dual strategy of recognition by peptidoglycan recognition protein, PGRP-S: structure of the ternary complex of PGRP-S with lipopolysaccharide and stearic acid

Peptidoglycan recognition proteins (PGRPs) are part of the innate immune system. The 19 kDa Short PGRP (PGRP-S) is one of the four mammalian PGRPs. The concentration of PGRP-S in camel (CPGRP-S) has been shown to increase considerably during mastitis. The structure of CPGRP-S consists of four protein molecules designated as A, B, C and D forming stable intermolecular contacts, A–B and C–D. The A–B and C–D interfaces are located on the opposite sides of the same monomer leading to the the formation of a linear chain with alternating A–B and C–D contacts. Two ligand binding sites, one at C–D contact and another at A–B contact have been observed. CPGRP-S binds to the components of bacterial cell wall molecules such as lipopolysaccharide (LPS), lipoteichoic acid (LTA), and peptidoglycan (PGN) from both Gram-positive and Gram-negative bacteria. It also binds to fatty acids including mycolic acid of the Mycobacterium tuberculosis (Mtb). Previous structural studies of binary complexes of CPGRP-S with LPS and stearic acid (SA) have shown that LPS binds to CPGRP-S at C–D contact (Site-1) while SA binds to it at the A–B contact (Site-2). The binding studies using surface plasmon resonance showed that LPS and SA bound to CPGRP-S in the presence of each other. The structure determination of the ternary complex showed that LPS and SA bound to CPGRP-S at Site-1 and Site-2 respectively. LPS formed 13 hydrogen bonds and 159 van der Waals contacts (distances ≤4.2 Å) while SA formed 56 van der Waals contacts. The ELISA test showed that increased levels of productions of pro-inflammatory cytokines TNF-α and IFN-γ due to LPS and SA decreased considerably upon the addition of CPGRP-S.