Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_150900,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 671
  Gunawardena S, Reddy GP, Wang YH, Kolli VSK, Orlando R, Morris JG, Bush CA "Structure of a muramic acid containing capsular polysaccharide from the pathogenic strain of Vibrio vulnificus ATCC27562" - Carbohydrate Research 309(1) (1998) 65-76
  

  Vibrio vulnificus strains isolated from septicemia cases and from the environment show a wide variety of capsular types. In an attempt to find common structural features which can be correlated with pathogenicity and toxicity, we have determined structures of the capsular polysaccharides (CPS) from several pathogenic strains. We report the complete structure of the polysaccharide from the pathogenic V. vulnificus strain ATCC27562 using a combination of homonuclear and heteronuclear one-dimensional and two dimensional NMR experiments. The 13C and 1H NMR spectra, including the exchangeable amide proton resonances, have been completely assigned. The amide linkage between Ser and C6 of GalA has been unambiguously determined by water-suppressed 2D NOESY. To verify the structure established by NMR, we have fragmented the polymer employing the Smith degradation procedure. The Smith product identified by NMR and matrix-assisted laser desorption mass spectrometry is consistent with the proposed structure for the CPS, which is composed of D-GlcNAc, MurNAc, D-GalA, L-Rha and is serine-linked as shown: [formula: see text]

  structure, mass spectrometry, Vibrio, Capsular polysaccaride, NMR spectrometry

  NCBI PubMed ID: 9720237
  Publication DOI: 10.1016/s0008-6215(98)00115-3
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bush@umbc.edu
  Institutions: Department of Chemistry and Biochemistry, University of Maryland Baltimore County 21250, USA, Complex carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 220 Riverbend Road, Athens, GA 30602-4712, USA, Departments of Medicine and Pathology, University of Maryland School of Medicine and Veterans Affairs Medical Center, Baltimore, MD 21201, USA
  Methods: NMR-2D, NMR, Smith degradation
  
   
  
  Vibrio vulnificus ATCC 27562
  CSDB ID 466 (all data & tools)
• Article ID: 5791
  Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" - Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
  

  Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.

  polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component

  Publication DOI: 10.1016/B978-0-12-819475-1.00005-5
  Publisher: Elsevier
  Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
  Editors: Barchi J, Kamerling H
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
  
   
  
  Vibrio vulnificus ATCC 27562
  CSDB ID 6665 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_150900,IEDB_151531

• Article ID: 671
  Gunawardena S, Reddy GP, Wang YH, Kolli VSK, Orlando R, Morris JG, Bush CA "Structure of a muramic acid containing capsular polysaccharide from the pathogenic strain of Vibrio vulnificus ATCC27562" - Carbohydrate Research 309(1) (1998) 65-76
  

  Vibrio vulnificus strains isolated from septicemia cases and from the environment show a wide variety of capsular types. In an attempt to find common structural features which can be correlated with pathogenicity and toxicity, we have determined structures of the capsular polysaccharides (CPS) from several pathogenic strains. We report the complete structure of the polysaccharide from the pathogenic V. vulnificus strain ATCC27562 using a combination of homonuclear and heteronuclear one-dimensional and two dimensional NMR experiments. The 13C and 1H NMR spectra, including the exchangeable amide proton resonances, have been completely assigned. The amide linkage between Ser and C6 of GalA has been unambiguously determined by water-suppressed 2D NOESY. To verify the structure established by NMR, we have fragmented the polymer employing the Smith degradation procedure. The Smith product identified by NMR and matrix-assisted laser desorption mass spectrometry is consistent with the proposed structure for the CPS, which is composed of D-GlcNAc, MurNAc, D-GalA, L-Rha and is serine-linked as shown: [formula: see text]

  structure, mass spectrometry, Vibrio, Capsular polysaccaride, NMR spectrometry

  NCBI PubMed ID: 9720237
  Publication DOI: 10.1016/s0008-6215(98)00115-3
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bush@umbc.edu
  Institutions: Department of Chemistry and Biochemistry, University of Maryland Baltimore County 21250, USA, Complex carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 220 Riverbend Road, Athens, GA 30602-4712, USA, Departments of Medicine and Pathology, University of Maryland School of Medicine and Veterans Affairs Medical Center, Baltimore, MD 21201, USA
  Methods: NMR-2D, NMR, Smith degradation
  
   
  
  Vibrio vulnificus ATCC 27562
  CSDB ID 575 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_1635957,IEDB_885814

• Article ID: 1367
  Bateman KP, Banoub JH, Thibault P "Probing the microheterogeneity of O-specific chains from Yersinia ruckeri using capillary zone electrophoresis/electrospray mass spectrometry" - Electrophoresis 17(12) (1996) 1818-1828
  

  Lipopolysaccharide, LPS, chain, O-specific, spectrometry, mass spectrometry, Yersinia, Capillary zone electrophoresis, electrospray mass spectrometry, microheterogeneity, Yersinia ruckeri

  Journal NLM ID: 8204476
  Publisher: Wiley-VCH
  Correspondence: pierre.thibault@nec.ca
  Institutions: Institute for Marine Biosciences, Nova Scotia, Canada
  Methods: CE-ESI-MS
  
   
  
  Yersinia ruckeri
  CSDB ID 6244 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: undecaprenol-Z8E3
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_1635957,IEDB_885814

• Article ID: 1616
  Guan Z, Breazeale SD, Raetz CR "Extraction and identification by mass spectrometry of undecaprenyl diphosphate-MurNAc-pentapeptide-GlcNAc from Escherichia coli" - Analytical Biochemistry 345(2) (2005) 336-339
  

  Undecaprenyl diphosphate-MurNAc-pentapeptide-GlcNAc (lipid II) is extracted from Escherichia coli cells by utilizing its unusual pH-dependent solubility property in a Bligh-Dyer system, and identified by electrospray ionization mass spectrometry in conjunction with a novel 15N mass shift analysis. The described approach will facilitate the structural characterization of lipid II variants from diverse bacteria, including antibiotic-resistant mutants, as well as the numerous minor uncharacterized lipids present in all biological systems

  Escherichia coli, mass spectrometry, Lipid II, 15N mass shift analysis

  NCBI PubMed ID: 16118008
  Publication DOI: 10.1016/j.ab.2005.07.002
  Journal NLM ID: 0370535
  Publisher: Academic Press
  Correspondence: zguan@biochem.duke.edu
  Institutions: Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
  Methods: ESI-MS
  
   
  
  Escherichia coli
  CSDB ID 10546 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: S-layer glycan
Contained glycoepitopes: IEDB_115015,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_142489,IEDB_143253,IEDB_149135,IEDB_151531,IEDB_225177,IEDB_885823,SB_86

• Article ID: 1623
  Kahlig H, Kolarich D, Zayni S, Scheberl A, Kosma P, Schäffer C, Messner P "N-Acetylmuramic acid as capping element of a-D-fucose-containing S-layer glycoprotein glycans from Geobacillus tepidamans GS5-97T" - Journal of Biological Chemistry 280(21) (2005) 20292-20299
  

  Geobacillus tepidamans GS5-97(T) is a novel Gram-positive, moderately thermophilic bacterial species that is covered by a glycosylated surface layer (S-layer) protein. The isolated and purified S-layer glycoprotein SgtA was ultrastructurally and chemically investigated and showed several novel properties. By SDS-PAGE, SgtA was separated into four distinct bands in an apparent molecular mass range of 106-166 kDa. The three high molecular mass bands gave a positive periodic acid-Schiff staining reaction, whereas the 106-kDa band was nonglycosylated. Glycosylation of SgtA was investigated by means of chemical analyses, 600-MHz nuclear magnetic resonance spectroscopy, and electrospray ionization quadrupole time-of-fight mass spectrometry. Glycopeptides obtained after Pronase digestion revealed the glycan structure [→2)-α-L-Rhap-(1→3)-α-D-Fucp-(1→](n=approximately 20), with D-fucopyranose having never been identified before as a constituent of S-layer glycans. The rhamnose residue at the nonreducing end of the terminal repeating unit of the glycan chain was di-substituted. For the first time, (R)-N-acetylmuramic acid, the key component of prokaryotic peptidoglycan, was found in an α-linkage to carbon 3 of the terminal rhamnose residue, serving as capping motif of an S-layer glycan. In addition, that rhamnose was substituted at position 2 with a β-N-acetylglucosamine residue. The S-layer glycan chains were bound via the trisaccharide core →2)-α-L-Rhap-(1→3)-α-L-Rhap-(1→3)-α-L-Rhap-(1→ to carbon 3 of β-D-galactose, which was attached in O-glycosidic linkage to serine and threonine residues of SgtA of G. tepidamans GS5-97(T).

  structure, mass spectrometry, glycosylation, Gram-positive, glycoprotein, D-fucose, Geobacillus, SgtA, S-layer glycan

  NCBI PubMed ID: 15781455
  Publication DOI: 10.1074/jbc.M501724200
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Institutions: Department of Organic Chemistry, University of Vienna, Austria
  Methods: NMR, sugar analysis, amino acid analysis, MS
  
   
  
  Geobacillus tepidamans GS5-97T
  CSDB ID 10723 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_1635957,IEDB_885814

• Article ID: 1778
  Knirel YA, Kochetkov NK "The structure of lipopolysaccharides of gram-negative bacteria. III. The structure of O-antigens: A review" - Biochemistry (Moscow) 59(12) (1994) 1325-1383
  

  This review summarizes data on the composition and structure of the O-antigens, the polysaccharide chains of the outer-membrane lipopolysaccharides (LPS) of Gram-negative bacteria defining the immunospecificity of these microbial cells. Special reference is given to some structural features of the O-antigens, such as the presence of unique monosaccharides and noncarbohydrate components, masked regularity, and the occurrence in one microorganism of LPS with structurally different polysaccharide chains. Antigenic relationships between microorganisms belonging to different taxonomic groups are discussed.

  structure, O-antigen, chemical composition, bacterial lipopolysaccharides, Salmonella livingstone C1

  NCBI PubMed ID: 7533007
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Yersinia ruckeri II
  CSDB ID 108436 (all data & tools)
• Article ID: 1798
  Banoub JH, Shaw DH, Pang H, Krepinsky JJ, Nakhla NA, Patel T "Structural elucidation of the O-specific antigen of Yersinia ruckeri by fast atom bombardment mass spectrometry (FAB-MS)" - Biomedical and Environmental Mass Spectrometry 19 (1990) 787-790
  
  NCBI PubMed ID: 2088577
  Journal NLM ID: 8603224
  Publisher: Wiley
  Institutions: Northwest Atlantic Fisheries Centre, St. John's, Newfoundland, Canada
  Methods: FAB-MS
  
   
  
  Yersinia ruckeri
  CSDB ID 110300 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: (1->O)peptide (the sequence was not not specified)
Trivial name: S-layer glycoprotein glycan
Compound class: glycan
Contained glycoepitopes: IEDB_115015,IEDB_135813,IEDB_136044,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_142489,IEDB_143253,IEDB_149135,IEDB_151531,IEDB_190606,IEDB_225177,IEDB_885823,SB_165,SB_166,SB_187,SB_195,SB_7,SB_86,SB_88

• Article ID: 3315
  Zayni S, Steiner K, Pfostl A, Hofinger A, Kosma P, Schäffer C, Messner P "The dTDP-4-dehydro-6-deoxyglucose reductase encoding fcd gene is part of the surface layer glycoprotein glycosylation gene cluster of Geobacillus tepidamans GS5-97T" - Glycobiology 17(4) (2007) 433-443
  

  The glycan chain of the S-layer protein of Geobacillus tepidamans GS5-97(T) consists of disaccharide repeating units composed of L-rhamnose and D-fucose, the latter being a rare constituent of prokaryotic glycoconjugates. Although biosynthesis of nucleotide-activated L-rhamnose is well established, D-fucose biosynthesis is less investigated. The conversion of α-D-glucose-1-phosphate into thymidine diphosphate (dTDP)-4-dehydro-6-deoxyglucose by the sequential action of RmlA (glucose-1-phosphate thymidylyltransferase) and RmlB (dTDP-glucose-4,6-dehydratase) is shared between the dTDP-D-fucose and the dTDP-L-rhamnose biosynthesis pathway. This key intermediate is processed by the dTDP-4-dehydro-6-deoxyglucose reductase Fcd to form dTDP-α-D-fucose. We identified the fcd gene in G. tepidamans GS5-97(T) by chromosome walking and performed functional characterization of the recombinant 308-amino acid enzyme. The in vitro activity of the enzymatic cascade (RmlB and Fcd) was monitored by high-performance liquid chromatography and the reaction product was confirmed by (1)H and (13)C nuclear magnetic resonance spectroscopy. This is the first characterization of the dTDP-α-D-fucopyranose biosynthesis pathway in a Gram-positive organism. fcd was identified as 1 of 20 open reading frames contained in a 17471-bp S-layer glycosylation (slg) gene cluster on the chromosome of G. tepidamans GS5-97(T). The sgtA structural gene is located immediately upstream of the slg gene cluster with an intergenic region of 247 nucleotides. By comparison of the SgtA amino acid sequence with the known glycosylation pattern of the S-layer protein SgsE of Geobacillus stearothermophilus NRS 2004/3a, two out of the proposed three glycosylation sites on SgtA could be identified by electrospray ionization quadrupole-time-of-flight mass spectrometry to be at positions Ser-792 and Thr-583

  glycosylation gene cluster, glycoprotein, surface layer glycoprotein, fcd, dTDP-4-dehydro-6-deoxyglucose reductase, Geobacillus tepidamans

  NCBI PubMed ID: 17202151
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Correspondence: paul.messner@boku.ac.at
  Institutions: Zentrum fur NanoBiotechnologie, Universitat fur Bodenkultur Wien, Vienna, Austria
  Methods: 13C NMR, 1H NMR, genetic methods, biochemical methods, HPLC, IR-MALDI-TOF MS
  
   
  
  Geobacillus tepidamans GS5-97T
  CSDB ID 22030 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: Thr583/Ser792 of S-layer protein
Trivial name: S-layer glycan
Contained glycoepitopes: IEDB_115015,IEDB_135813,IEDB_136044,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_142489,IEDB_143253,IEDB_149135,IEDB_151531,IEDB_190606,IEDB_225177,IEDB_885823,SB_165,SB_166,SB_187,SB_195,SB_7,SB_86,SB_88

• Article ID: 3517
  Messner P, Steiner K, Zarschler K, Schäffer C "S-layer nanoglycobiology of bacteria" - Carbohydrate Research 343(12) (2008) 1934-1951
  

  Cell surface layers (S-layers) are common structures of the bacterial cell envelope with a lattice-like appearance that are formed by a self-assembly process. Frequently, the constituting S-layer proteins are modified with covalently linked glycan chains facing the extracellular environment. S-layer glycoproteins from organisms of the Bacillaceae family possess long, O-glycosidically linked glycans that are composed of a great variety of sugar constituents. The observed variations already exceed the display found in eukaryotic glycoproteins. Recent investigations of the S-layer protein glycosylation process at the molecular level, which has lagged behind the structural studies due to the lack of suitable molecular tools, indicated that the S-layer glycoprotein glycan biosynthesis pathway utilizes different modules of the well-known biosynthesis routes of lipopolysaccharide O-antigens. The genetic information for S-layer glycan biosynthesis is usually present in S-layer glycosylation (slg) gene clusters acting in concert with housekeeping genes. To account for the nanometer-scale cell surface display feature of bacterial S-layer glycosylation, we have coined the neologism 'nanoglycobiology'. It includes structural and biochemical aspects of S-layer glycans as well as molecular data on the machinery underlying the glycosylation event. A key aspect for the full potency of S-layer nanoglycobiology is the unique self-assembly feature of the S-layer protein matrix. Being aware that in many cases the glycan structures associated with a protein are the key to protein function, S-layer protein glycosylation will add a new and valuable component to an 'S-layer based molecular construction kit'. In our long-term research strategy, S-layer nanoglycobiology shall converge with other functional glycosylation systems to produce 'functional' S-layer neoglycoproteins for diverse applications in the fields of nanobiotechnology and vaccine technology. Recent advances in the field of S-layer nanoglycobiology have made our overall strategy a tangible aim of the near future

  glycosylation gene cluster, S-layer glycoprotein, Glycosylation enzymes, Nanobiotechnology, Carbohydrate engineering, Self-assembly

  NCBI PubMed ID: 18336801
  Publication DOI: 10.1016/j.carres.2007.12.025
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: paul.messner@boku.ac.at; christina.schaeffer@boku.ac.at
  Institutions: Universitat fur Bodenkultur Wien, Zentrum fur NanoBiotechnologie A-1180 Wien, Gregor-Mendel-Strasse 33, Austria
  Methods: 13C NMR, 1H NMR, NMR-2D, chemical methods, MS, NMR-1D, serological methods, genetic methods, biochemical methods
  
   
  
  Geobacillus tepidamans GS5-97T (DSM 16325T)
  CSDB ID 23139 (all data & tools)

Show legend Show as text

Structure type: monomer
Aglycon: undecaprenol
Contained glycoepitopes: IEDB_135813,IEDB_136017,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_1635957,IEDB_885814

• Article ID: 3767
  Rangarajan ES, Proteau A, Cui Q, Logan SM, Potetinova Z, Whitfield D, Purisima EO, Cygler M, Matte A, Sulea T, Schoenhofen IC "Structural and Functional Analysis of Campylobacter jejuni PseG: A UDP-sugar hydrolase from the pseudaminic acid biosynthetic pathway" - Journal of Biological Chemistry 284(31) (2009) 20989-21000
  

  Flagella of the bacteria Helicobacter pylori and Campylobacter jejuni are important virulence determinants, whose proper assembly and function are dependent upon glycosylation at multiple positions by sialic acid-like sugars, such as 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-nonulosonic acid (pseudaminic acid (Pse)). The fourth enzymatic step in the pseudaminic acid pathway, the hydrolysis of UDP-2,4-diacetamido-2,4,6-trideoxy-β-L-altropyranose to generate 2,4-diacetamido-2,4,6-trideoxy-l-altropyranose, is performed by the nucleotide sugar hydrolase PseG. To better understand the molecular basis of the PseG catalytic reaction, we have determined the crystal structures of C. jejuni PseG in apo-form and as a complex with its UDP product at 1.8 and 1.85 A resolution, respectively. In addition, molecular modeling was utilized to provide insight into the structure of the PseG-substrate complex. This modeling identifies a His(17)-coordinated water molecule as the putative nucleophile and suggests the UDP-sugar substrate adopts a twist-boat conformation upon binding to PseG, enhancing the exposure of the anomeric bond cleaved and favoring inversion at C-1. Furthermore, based on these structures a series of amino acid substitution derivatives were constructed, altering residues within the active site, and each was kinetically characterized to examine its contribution to PseG catalysis. In conjunction with structural comparisons, the almost complete inactivation of the PseG H17F and H17L derivatives suggests that His(17) functions as an active site base, thereby activating the nucleophilic water molecule for attack of the anomeric C-O bond of the UDP-sugar. As the PseG structure reveals similarity to those of glycosyltransferase family-28 members, in particular that of Escherichia coli MurG, these findings may also be of relevance for the mechanistic understanding of this important enzyme family.

  Campylobacter jejuni, pseudaminic acid, crystal structure, Helicobacter pylori, glycosyltransferase, modeling, hydrolase, flagella

  NCBI PubMed ID: 19483088
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: traian.sulea@nrc-cnrc.gc.ca; ian.schoenhofen@nrc-cnrc.gc.ca
  Institutions: From the Department of Biochemistry, McGill University, Montreal, Quebec H3G 1V6
  Methods: X-ray, SDS-PAGE, MD simulations, genetic methods, molecular modeling, CD, crystallization
  
   
  
  Escherichia coli
  CSDB ID 24196 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: peptidoglycan
Trivial name: secondary cell wall polymer
Compound class: cell wall polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_137340,IEDB_137473,IEDB_141807,IEDB_150077,IEDB_151531,IEDB_885813

• Article ID: 4397
  Steindl C, Schäffer C, Wugeditsch T, Graninger M, Matecko I, Müller N, Messner P "The first biantennary bacterial secondary cell wall polymer and its influence on S-layer glycoprotein assembly" - Biochemical Journal (2002) 483-494
  

  The cell surface of Aneurinibacillus thermoaerophilus DSM 10155 is covered with a square surface (S)-layer glycoprotein lattice. This S-layer glycoprotein, which was extracted with aqueous buffers after a freeze-thaw cycle of the bacterial cells, is the only completely water-soluble S-layer glycoprotein to be reported to date. The purified S-layer glycoprotein preparation had an overall carbohydrate content of 19%. Detailed chemical investigations indicated that the S-layer O-glycans of previously established structure accounted for 13% of total glycosylation. The remainder could be attributed to a peptidoglycan-associated secondary cell wall polymer. Structure analysis was performed using purified secondary cell wall polymer-peptidoglycan complexes. NMR spectroscopy revealed the first biantennary secondary cell wall polymer from the domain Bacteria, with the structure α-D-GlcpNAc-(1→3)-β-D-ManpNAc-(1→4)-β-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1→3)-β-D-ManpNAc-(1→4)-β-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1→4)-[α-D-GlcpNAc-(1→3)-β-D-ManpNAc-(1→4)-β-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1→3)-β-D-ManpNAc-(1→4)-β-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1→3)]-β-D-ManpNAc-(1→3)-α-D-GlcpNAc-(1→3)-β-D-ManpNAc-(1→3)-α-D-GlcpNAc-(1→3)-α-D-GlcpNAc-(1→O)-PO(2)(-)-O-PO(2)(-)-(O→6)-MurNAc- (where MurNAc is N-acetylmuramic acid). The neutral polysaccharide is linked via a pyrophosphate bond to the C-6 atom of every fourth N-acetylmuramic acid residue, in average, of the A1γ-type peptidoglycan. In vivo, the biantennary polymer anchored the S-layer glycoprotein very effectively to the cell wall, probably due to the doubling of motifs for a proposed lectin-like binding between the polymer and the N-terminus of the S-layer protein. When the cellular support was removed during S-layer glycoprotein isolation, the co-purified polymer mediated the solubility of the S-layer glycoprotein in vitro. Initial crystallization experiments performed with the soluble S-layer glycoprotein revealed that the assembly property could be restored upon dissociation of the polymer by the addition of poly(ethylene glycols). The formed two-dimensional crystalline S-layer self-assembly products exhibited the same lattice symmetry as observed on intact bacterial cells.

  NMR spectroscopy, bacteria, Structure determination, biantennary peptidoglycan-associated polymer

  NCBI PubMed ID: 12201818
  Publication DOI: 10.1042/BJ20020988
  Journal NLM ID: 2984726R
  Publisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
  Correspondence: CRS@edv1.boku.ac.at
  Institutions: Institut fur Chemie, Johannes-Kepler-Universitat Linz, A-4040 Linz, Austria
  Methods: 13C NMR, 1H NMR, SDS-PAGE, sugar analysis, 31P NMR, ESI-TOF-MS
  
   
  
  Aneurinibacillus thermoaerophilus DSM 10155
  CSDB ID 27325 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: LOS
Contained glycoepitopes: IEDB_130650,IEDB_136044,IEDB_136105,IEDB_137472,IEDB_141794,IEDB_141806,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_153543,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88

• Article ID: 4839
  Casillo A, Parrilli E, Filomena S, Lindner B, Lanzetta R, Parrilli M, Tutino ML, Corsaro MM "Structural Investigation of the Oligosaccharide Portion Isolated from the Lipooligosaccharide of the Permafrost Psychrophile Psychrobacter arcticus 273-4" - Marine Drugs 13(7) (2015) 4539-4555
  

  Psychrophilic microorganisms have successfully colonized all permanently cold environments from the deep sea to mountain and polar regions. The ability of an organism to survive and grow in cryoenviroments depends on a number of adaptive strategies aimed at maintaining vital cellular functions at subzero temperatures, which include the structural modifications of the membrane. To understand the role of the membrane in the adaptation, it is necessary to characterize the cell-wall components, such as the lipopolysaccharides, that represent the major constituent of the outer membrane. The aim of this study was to investigate the structure of the carbohydrate backbone of the lipooligosaccharide (LOS) isolated from the cold-adapted Psychrobacter arcticus 273-4. The strain, isolated from a 20,000-to-30,000-year-old continuously frozen permafrost in Siberia, was cultivated at 4 degrees C. The LOS was isolated from dry cells and analyzed by means of chemical methods. In particular, it was degraded either by mild acid hydrolysis or by hydrazinolysis and investigated in detail by (1)H and (13)C NMR spectroscopy and by ESI FT-ICR mass spectrometry. The oligosaccharide was characterized by the substitution of the heptose residue, usually linked to Kdo in the inner core, with a glucose, and for the unusual presence of N-acetylmuramic acid.

  Lipopolysaccharide, structural determination, glycoconjugates, NMR spectroscopy, N-acetylmuramic acid, Psychrobacter arcticus strain 273-4

  NCBI PubMed ID: 26204948
  Publication DOI: 10.3390/md13074539
  Journal NLM ID: 101213729
  Publisher: Basel, Switzerland: Molecular Diversity Preservation International
  Correspondence: corsaro@unina.it
  Institutions: Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, Napoli 80126, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, Napoli 80131, Italy, Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 10, BorstelD-23845, Germany, Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, Napoli 80126, Italy
  Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, sugar analysis, mild acid hydrolysis, ESI-ICR-MS, GC, de-O-acylation with hydrazine, NMR-1D, methanolysis, reduction with NaBD4
  
   
  
  Psychrobacter arcticus 273-4
  CSDB ID 11008 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130658,IEDB_130659,IEDB_135394,IEDB_136044,IEDB_136105,IEDB_137472,IEDB_137777,IEDB_140956,IEDB_141794,IEDB_141806,IEDB_141807,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_153543,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88

• Article ID: 5411
  Casillo A, Parrilli E, Tutino ML, Corsaro MM "The outer membrane glycolipids of bacteria from cold environments: isolation, characterization, and biological activity" - FEMS Microbiology Ecology 95(7) (2019) fiz094
  

  Lipopolysaccharides (LPSs) are the main components of the external leaflet of the outer membrane of Gram-negative bacteria. Microorganisms that colonize permanently or transiently cold habitats have evolved an array of structural adaptations, some of which involve components of bacterial membranes. These adaptations assure the perfect functionality of the membrane even at freezing or sub-freezing growth temperatures. This review summarizes the state-of-the-art information concerning the structural features of the LPSs produced by cold-adapted bacteria. The LPS structure has recently been elucidated from species mainly belonging to Gammaproteobacteria and Flavobacteriaceae. Although the reported structural heterogeneity may arise from the phylogenetic diversity of the analyzed source strains, some generalized trends can be deduced. For instance, it is clear that only a small portion of LPSs displays the O-chain. In addition, the biological activity of the lipid A portion from several cold-adapted strains is reported.

  structure, lipid A, outer membrane, Cold adaptation, isolation and characterization, Rough-LPS, smooth-LPS

  NCBI PubMed ID: 31210256
  Publication DOI: 10.1093/femsec/fiz094
  Journal NLM ID: 8901229
  Publisher: Oxford University Press
  Correspondence: corsaro@unina.it
  Institutions: Department of Chemical Sciences, Universitá degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
  
   
  
  Psychrobacter arcticus 273-4
  CSDB ID 642 (all data & tools)

Show legend Show as text

Structure type: monomer
Compound class: glycopeptide

• Article ID: 5685
  Moraes GL, Gomes GC, de Sousa PRM, Alves CN, Govender T, Kruger HG, Maguire GE, Lamichhane G, Lameira J "Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development" - Tuberculosis 95(2) (2015) 95-111
  

  Tuberculosis (TB) is the second leading cause of human mortality from infectious diseases worldwide. The WHO reported 1.3 million deaths and 8.6 million new cases of TB in 2012. Mycobacterium tuberculosis (M. tuberculosis), the infectious bacteria that causes TB, is encapsulated by a thick and robust cell wa11. The innermost segment of the cell wall is comprised of peptidoglycan, a layer that is required for survival and growth of the pathogen. Enzymes that catalyse biosynthesis of the peptidoglycan are essential and are therefore attractive targets for discovery of novel antibiotics as humans lack similar enzymes making it possible to selectively target bacteria only. In this paper, we have reviewed the structures and functions of enzymes GlmS, GlmM, GlmU, MurA, MurB, MurC, MurD, MurE and MurF from M. tuberculosis that are involved in peptidoglycan biosynthesis. In addition, we report homology modelled 3D structures of those key enzymes from M. tuberculosis of which the structures are still unknown. We demonstrated that natural substrates can be successfully docked into the active sites of the GlmS and GlmU respectively. It is therefore expected that the models and the data provided herein will facilitate translational research to develop new drugs to treat TB

  peptidoglycan, Drug design, homology modelling, TB

  NCBI PubMed ID: 25701501
  Publication DOI: 10.1016/j.tube.2015.01.006
  Journal NLM ID: 100971555
  Publisher: Edinburgh, New York: Churchill Livingstone
  Correspondence: lameira@ufpa.br
  Institutions: Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil, Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa, Johns Hopkins University School of Medicine, Taskforce to Study Resistance Emergence & Antimicrobial Development Technology, Baltimore, USA
  
   
  
  Mycobacterium tuberculosis
  CSDB ID 49316 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Compound class: peptidoglycan
Contained glycoepitopes: IEDB_135813,IEDB_136017,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_1635957,IEDB_177375,IEDB_885814

• Article ID: 5833
  Queda F, Covas G, Filipe SR, Marques MMB "Assembly of Peptidoglycan Fragments-A Synthetic Challenge" - Pharmaceuticals 13(11) (2020) 392
  

  Peptidoglycan (PGN) is a major constituent of most bacterial cell walls that is recognized as a primary target of the innate immune system. The availability of pure PGN molecules has become key to different biological studies. This review aims to (1) provide an overview of PGN biosynthesis, focusing on the main biosynthetic intermediates; (2) focus on the challenges for chemical synthesis posed by the unique and complex structure of PGN; and (3) cover the synthetic routes of PGN fragments developed to date. The key difficulties in the synthesis of PGN molecules mainly involve stereoselective glycosylation involving NAG derivatives. The complex synthesis of the carbohydrate backbone commonly involves multistep sequences of chemical reactions to install the lactyl moiety at the O-3 position of NAG derivatives and to control enantioselective glycosylation. Recent advances are presented and synthetic routes are described according to the main strategy used: (i) based on the availability of starting materials such as glucosamine derivatives; (ii) based on a particular orthogonal synthesis; and (iii) based on the use of other natural biopolymers as raw materials.

  Pathogenesis, Bacterial, cell, surface, cell surface, bacterial peptidoglycan, NAG-NAM disaccharide, PGN biosynthesis, PGN synthesis

  NCBI PubMed ID: 33203094
  Publication DOI: 10.3390/ph13110392
  Journal NLM ID: 101238453
  Publisher: Basel, Switzerland: MDPI
  Correspondence: sfilipe@fct.unl.pt; mmbmarques@fct.unl.pt
  Institutions: LAQV@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, Caparica, Portugal, UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, Caparica, Portugal, Laboratory of Bacterial Cell Surfaces and Pathogenesis, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
  
   
  
  Staphylococcus aureus
  CSDB ID 32185 (all data & tools)