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Peptidoglycan recognition protein 3

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PGLYRP3
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesPGLYRP3, PGRP-Ialpha, PGRPIA, PGLYRPIalpha, peptidoglycan recognition protein 3
External IDsOMIM: 608197; MGI: 2685266; HomoloGene: 71559; GeneCards: PGLYRP3; OMA:PGLYRP3 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

114771

242100

Ensembl

ENSG00000159527

ENSMUSG00000042244

UniProt

Q96LB9

A1A547

RefSeq (mRNA)

NM_052891

NM_207247

RefSeq (protein)

NP_443123

NP_997130

Location (UCSC)Chr 1: 153.3 – 153.31 MbChr 3: 91.92 – 91.94 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse
Location of human PGLYRP3 gene on chromosome 1 and schematic gene, cDNA, and protein structures with exons, introns, and protein domains indicated.

Peptidoglycan recognition protein 3 (PGLYRP3, formerly PGRP-Iα) is an antibacterial and anti-inflammatory innate immunity protein that in humans is encoded by the PGLYRP3 gene.[5][6][7][8]

Discovery

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PGLYRP3 (formerly PGRP-Iα), a member of a family of human Peptidoglycan Recognition Proteins (PGRPs), was discovered in 2001 by Roman Dziarski and coworkers who cloned and identified the genes for three human PGRPs, PGRP-L, PGRP-Iα, and PGRP-Iβ (named for long and intermediate size transcripts),[5] and established that human genome codes for a family of 4 PGRPs: PGRP-S (short PGRP or PGRP-S)[9] and PGRP-L, PGRP-Iα, and PGRP-Iβ.[5] Subsequently, the Human Genome Organization Gene Nomenclature Committee changed the gene symbols of PGRP-S, PGRP-L, PGRP-Iα, and PGRP-Iβ to PGLYRP1 (peptidoglycan recognition protein 1), PGLYRP2 (peptidoglycan recognition protein 2), PGLYRP3 (peptidoglycan recognition protein 3), and PGLYRP4 (peptidoglycan recognition protein 4), respectively, and this nomenclature is currently also used for other mammalian PGRPs.

Tissue distribution and secretion

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PGLYRP3 has similar expression to PGLYRP4 (peptidoglycan recognition protein 4) but not identical.[5][6] PGLYRP3 is constitutively expressed in the skin, in the eye, and in the mucous membranes in the tongue, throat, and esophagus, and at a much lower level in the remaining parts of the intestinal tract.[5][6][10][11] Bacteria and their products increase the expression of PGLYRP3 in keratinocytes and oral epithelial cells.[6][12] Mouse PGLYRP3 is also differentially expressed in the developing brain and this expression is influenced by the intestinal microbiome.[13] PGLYRP3 is secreted and forms disulfide-linked dimers.[6]

Structure

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PGLYRP3, similar to PGLYRP4, has two peptidoglycan-binding type 2 amidase domains (also known as PGRP domains), which are not identical (have 38% amino acid identity in humans)[5][14] and do not have amidase enzymatic activity.[15] PGLYRP3 is secreted, it is glycosylated, and its glycosylation is required for its bactericidal activity.[6] PGLYRP3 forms disulfide-linked homodimers, but when expressed in the same cells with PGLYRP4, it forms PGLYRP3:PGLYRP4 disulfide-linked heterodimers.[6]

The C-terminal peptidoglycan-binding domain of human PGLYRP3 has been crystallized and its structure solved[16] and is similar to human PGLYRP1.[17] PGLYRP3 C-terminal PGRP domain contains a central β-sheet composed of five β-strands and three α-helices and N-terminal segment unique to PGRPs and not found in bacteriophage and prokaryotic amidases.[16]

Human PGLYRP3 C-terminal PGRP domain, similar to PGLYRP1,[17] has three pairs of cysteines, which form three disulfide bonds at positions 178–300, 194–238, and 214–220.[16] The Cys214–Cys220 disulfide is broadly conserved in invertebrate and vertebrate PRGPs, the Cys178–Cys300 disulfide is conserved in all mammalian PGRPs, and the Cys194–238 disulfide is unique to mammalian PGLYRP1, PGLYRP3, and PGLYRP4, but not found in the amidase-active PGLYRP2.[5][15][16][17] The structures of the entire PGLYRP3 molecule (with two PGRP domains) and of the disulfide-linked dimer are unknown.

PGLYRP3 C-terminal PGRP domain contains peptidoglycan-binding site, which is a long cleft whose walls are formed by α-helix and five β-loops and the floor by a β-sheet. This site binds muramyl-tripeptide (MurNAc-L-Ala-D-isoGln-L-Lys), but can also accommodate larger peptidoglycan fragments, such as disaccharide-pentapeptide.[18] Located opposite the peptidoglycan-binding cleft is a large hydrophobic groove, formed by residues 177–198 (the PGRP-specific segment).[18]

Functions

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The PGLYRP3 protein plays an important role in the innate immune responses.

Peptidoglycan binding

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PGLYRP3 binds peptidoglycan, a polymer of β(1-4)-linked N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) cross-linked by short peptides, the main component of bacterial cell wall.[5][6][18][19][20] The smallest peptidoglycan fragment that binds to human PGLYRP3 is MurNAc-tripeptide (MurNAc-L-Ala-D-isoGln-L-Lys), which binds with low affinity (Kd = 4.5 x 10−4 M), whereas a larger fragment, MurNAc-pentapeptide (MurNAc-L-Ala-γ-D-Gln-L-Lys-D-Ala-D-Ala), binds with higher affinity (Kd = 6 x 10-6  M).[19][20][21] Human PGLYRP3, in contrast to PGLYRP1, does not bind meso-diaminopimelic acid (m-DAP) containing fragment (MurNAc-L-Ala-γ-D-Gln-DAP-D-Ala-D-Ala).[19][20][21] m-DAP is present in the third position of peptidoglycan peptide in Gram-negative bacteria and Gram-positive bacilli, whereas L-lysine is in this position in peptidoglycan peptide in Gram-positive cocci. Thus, PGLYRP3 C-terminal PGRP domain has a preference for binding peptidoglycan fragments from Gram-positive cocci. Binding of MurNAc-pentapeptide induces structural rearrangements in the binding site that are essential for entry of the ligand and locks the ligand in the binding cleft.[22] The fine specificity of the PGLYRP3 N-terminal PGRP domain is not known.

Bactericidal activity

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Human PGLYRP3 is directly bactericidal for both Gram-positive (Bacillus subtilis, Bacillus licheniformis, Bacillus cereus, Lactobacillus acidophilus, Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes) and Gram-negative (Escherichia coli, Proteus vulgaris, Salmonella enterica, Shigella sonnei, Pseudomonas aeruginosa) bacteria.[6][23][24][25]

The mechanism of bacterial killing by PGLYRP3 is based on induction of lethal envelope stress, which eventually leads to the shutdown of transcription and translation.[24] PGLYRP3-induced killing involves simultaneous induction of three stress responses in both Gram-positive and Gram-negative bacteria: oxidative stress due to production of reactive oxygen species (hydrogen peroxide and hydroxyl radicals), thiol stress due to depletion (oxidation) of cellular thiols, and metal stress due to an increase in intracellular free (labile) metal ions.[24][25] PGLYRP3-induced bacterial killing does not involve cell membrane permeabilization, which is typical for defensins and other antimicrobial peptides, cell wall hydrolysis, or osmotic shock.[6][23][24] Human PGLYRP3 has synergistic bactericidal activity with antibacterial peptides.[23]

Defense against infections

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PGLYRP3 plays a limited role in host defense against infections. Intranasal administration of PGLYRP3 protects mice from lung infection with S. aureus and E. coli,[6][26] but PGLYRP3-deficient mice do not have altered sensitivity to Streptococcus pneumoniae-induced pneumonia.[27]

Maintaining microbiome

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Mouse PGLYRP3 plays a role in maintaining healthy microbiome, as PGLYRP3-deficient mice have significant changes in the composition of their intestinal microbiome, which affect their sensitivity to colitis.[11][28][29]

Effects on inflammation

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Mouse PGLYRP3 plays a role in maintaining anti- and pro-inflammatory homeostasis in the intestine and skin. PGLYRP3-deficient mice are more sensitive than wild type mice to dextran sodium sulfate (DSS)-induced colitis, which indicates that PGLYRP3 protects mice from DSS-induced colitis.[11][29] The anti-inflammatory effect of PGLYRP3 on DSS-induced colitis depends on the PGLYRP3-regulated intestinal microbiome, because this greater sensitivity of PGLYRP3-deficient mice to DSS-induced colitis could be transferred to wild type germ-free mice or to antibiotic-treated mice by microbiome transplant from PGLYRP3-deficient mice[11][29] or by PGLYRP3-regulated bacteria.[28] PGLYRP3 is also directly anti-inflammatory in intestinal epithelial cells.[30][31][32]

PGLYRP3-deficient mice are more sensitive than wild type mice to experimentally induced atopic dermatitis.[33] These results indicate that mouse PGLYRP3 is anti-inflammatory and protects skin from inflammation. This anti-inflammatory effect is due to decreased numbers and activity of T helper 17 (Th17) cells and increased numbers of T regulatory (Treg) cells.[33]

Medical relevance

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Genetic PGLYRP3 variants are associated with some diseases. Patients with inflammatory bowel disease (IBD), which includes Crohn's disease and ulcerative colitis, have significantly more frequent missense variants in PGLYRP3 gene (and also in the other three PGLYRP genes) than healthy controls.[14] PGLYRP3 variants are also associated with Parkinson's disease[34] and psoriasis.[35][36] These results suggest that PGLYRP3 protects humans from these diseases, and that mutations in PGLYRP3 gene are among the genetic factors predisposing to these diseases. PGLYRP3 variants are also associated with the composition of airway microbiome.[37]

See also

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References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000159527 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000042244 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
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  6. ^ a b c d e f g h i j k Lu X, Wang M, Qi J, Wang H, Li X, Gupta D, Dziarski R (March 2006). "Peptidoglycan recognition proteins are a new class of human bactericidal proteins". The Journal of Biological Chemistry. 281 (9): 5895–907. doi:10.1074/jbc.M511631200. PMID 16354652. S2CID 21943426.
  7. ^ "PGLYRP3 peptidoglycan recognition protein 3 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-11-02.
  8. ^ "PGLYRP3 - Peptidoglycan recognition protein 3 precursor - Homo sapiens (Human) - PGLYRP3 gene & protein". www.uniprot.org. Retrieved 2020-11-02.
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  15. ^ a b Wang ZM, Li X, Cocklin RR, Wang M, Wang M, Fukase K, et al. (December 2003). "Human peptidoglycan recognition protein-L is an N-acetylmuramoyl-L-alanine amidase". The Journal of Biological Chemistry. 278 (49): 49044–52. doi:10.1074/jbc.M307758200. PMID 14506276. S2CID 35373818.
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  19. ^ a b c Kumar S, Roychowdhury A, Ember B, Wang Q, Guan R, Mariuzza RA, Boons GJ (November 2005). "Selective recognition of synthetic lysine and meso-diaminopimelic acid-type peptidoglycan fragments by human peptidoglycan recognition proteins I{alpha} and S". The Journal of Biological Chemistry. 280 (44): 37005–12. doi:10.1074/jbc.M506385200. PMID 16129677. S2CID 44913130.
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  21. ^ a b Cho S, Wang Q, Swaminathan CP, Hesek D, Lee M, Boons GJ, et al. (May 2007). "Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins". Proceedings of the National Academy of Sciences of the United States of America. 104 (21): 8761–6. Bibcode:2007PNAS..104.8761C. doi:10.1073/pnas.0701453104. PMC 1885576. PMID 17502600.
  22. ^ Guan R, Brown PH, Swaminathan CP, Roychowdhury A, Boons GJ, Mariuzza RA (May 2006). "Crystal structure of human peptidoglycan recognition protein I alpha bound to a muramyl pentapeptide from Gram-positive bacteria". Protein Science. 15 (5): 1199–206. doi:10.1110/ps.062077606. PMC 2242522. PMID 16641493.
  23. ^ a b c Wang M, Liu LH, Wang S, Li X, Lu X, Gupta D, Dziarski R (March 2007). "Human peptidoglycan recognition proteins require zinc to kill both gram-positive and gram-negative bacteria and are synergistic with antibacterial peptides". Journal of Immunology. 178 (5): 3116–25. doi:10.4049/jimmunol.178.5.3116. PMID 17312159. S2CID 22160694.
  24. ^ a b c d Kashyap DR, Wang M, Liu LH, Boons GJ, Gupta D, Dziarski R (June 2011). "Peptidoglycan recognition proteins kill bacteria by activating protein-sensing two-component systems". Nature Medicine. 17 (6): 676–83. doi:10.1038/nm.2357. PMC 3176504. PMID 21602801.
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  26. ^ Dziarski R, Kashyap DR, Gupta D (June 2012). "Mammalian peptidoglycan recognition proteins kill bacteria by activating two-component systems and modulate microbiome and inflammation". Microbial Drug Resistance. 18 (3): 280–5. doi:10.1089/mdr.2012.0002. PMC 3412580. PMID 22432705.
  27. ^ Shrivastav A, Dabrowski AN, Conrad C, Baal N, Hackstein H, Plog S, et al. (2018). "Peptidoglycan Recognition Protein 3 Does Not Alter the Outcome of Pneumococcal Pneumonia in Mice". Frontiers in Microbiology. 9: 103. doi:10.3389/fmicb.2018.00103. PMC 5799233. PMID 29449834.
  28. ^ a b Dziarski R, Park SY, Kashyap DR, Dowd SE, Gupta D (2016). "Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice". PLOS ONE. 11 (1): e0146162. Bibcode:2016PLoSO..1146162D. doi:10.1371/journal.pone.0146162. PMC 4699708. PMID 26727498.
  29. ^ a b c Jing X, Zulfiqar F, Park SY, Núñez G, Dziarski R, Gupta D (September 2014). "Peptidoglycan recognition protein 3 and Nod2 synergistically protect mice from dextran sodium sulfate-induced colitis". Journal of Immunology. 193 (6): 3055–69. doi:10.4049/jimmunol.1301548. PMC 4157132. PMID 25114103.
  30. ^ Zenhom M, Hyder A, Kraus-Stojanowic I, Auinger A, Roeder T, Schrezenmeir J (June 2011). "PPARγ-dependent peptidoglycan recognition protein 3 (PGlyRP3) expression regulates proinflammatory cytokines by microbial and dietary fatty acids". Immunobiology. 216 (6): 715–24. doi:10.1016/j.imbio.2010.10.008. PMID 21176858.
  31. ^ Zenhom M, Hyder A, de Vrese M, Heller KJ, Roeder T, Schrezenmeir J (April 2012). "Peptidoglycan recognition protein 3 (PglyRP3) has an anti-inflammatory role in intestinal epithelial cells". Immunobiology. 217 (4): 412–9. doi:10.1016/j.imbio.2011.10.013. PMID 22099350.
  32. ^ Zenhom M, Hyder A, de Vrese M, Heller KJ, Roeder T, Schrezenmeir J (May 2011). "Prebiotic oligosaccharides reduce proinflammatory cytokines in intestinal Caco-2 cells via activation of PPARγ and peptidoglycan recognition protein 3". The Journal of Nutrition. 141 (5): 971–7. doi:10.3945/jn.110.136176. PMID 21451128.
  33. ^ a b Park SY, Gupta D, Kim CH, Dziarski R (2011). "Differential effects of peptidoglycan recognition proteins on experimental atopic and contact dermatitis mediated by Treg and Th17 cells". PLOS ONE. 6 (9): e24961. Bibcode:2011PLoSO...624961P. doi:10.1371/journal.pone.0024961. PMC 3174980. PMID 21949809.
  34. ^ Goldman SM, Kamel F, Ross GW, Jewell SA, Marras C, Hoppin JA, et al. (August 2014). "Peptidoglycan recognition protein genes and risk of Parkinson's disease". Movement Disorders. 29 (9): 1171–80. doi:10.1002/mds.25895. PMC 4777298. PMID 24838182.
  35. ^ Sun C, Mathur P, Dupuis J, Tizard R, Ticho B, Crowell T, et al. (March 2006). "Peptidoglycan recognition proteins Pglyrp3 and Pglyrp4 are encoded from the epidermal differentiation complex and are candidate genes for the Psors4 locus on chromosome 1q21". Human Genetics. 119 (1–2): 113–25. doi:10.1007/s00439-005-0115-8. PMID 16362825. S2CID 31486449.
  36. ^ Kainu K, Kivinen K, Zucchelli M, Suomela S, Kere J, Inerot A, et al. (February 2009). "Association of psoriasis to PGLYRP and SPRR genes at PSORS4 locus on 1q shows heterogeneity between Finnish, Swedish and Irish families". Experimental Dermatology. 18 (2): 109–15. doi:10.1111/j.1600-0625.2008.00769.x. PMID 18643845. S2CID 5771478.
  37. ^ Igartua C, Davenport ER, Gilad Y, Nicolae DL, Pinto J, Ober C (February 2017). "Host genetic variation in mucosal immunity pathways influences the upper airway microbiome". Microbiome. 5 (1): 16. doi:10.1186/s40168-016-0227-5. PMC 5286564. PMID 28143570.

Further reading

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