Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_151528,IEDB_190606,IEDB_2189047,IEDB_225177,IEDB_226811,IEDB_232584,IEDB_885823,IEDB_983931,SB_192,SB_7

• Article ID: 81
  Frirdich E, Lindner B, Holst O, Whitfield C "Overexpression of the waaZ gene leads to modification of the structure of the inner core region of Escherichia coli lipopolysaccharide, truncation of the outer core, and reduction of the amount of O polysaccharide on the cell surface" - Journal of Bacteriology 185(5) (2003) 1659-1671
  

  The waa gene cluster is responsible for the biosynthesis of the lipopolysaccharide (LPS) core region in Escherichia coli and Salmonella: Homologs of the waaZ gene product are encoded by the waa gene clusters of Salmonella enterica and E. coli strains with the K-12 and R2 core types. Overexpression of WaaZ in E. coli and S. enterica led to a modified LPS structure showing core truncations and (where relevant) to a reduction in the amount of O-polysaccharide side chains. Mass spectrometry and nuclear magnetic resonance spectroscopy were used to determine the predominant LPS structures in an E. coli isolate with an R1 core (waaZ is lacking from the type R1 waa gene cluster) with a copy of the waaZ gene added on a plasmid. Novel truncated LPS structures, lacking up to 3 hexoses from the outer core, resulted from WaaZ overexpression. The truncated molecules also contained a KdoIII residue not normally found in the R1 core

  Lipopolysaccharide, biosynthesis, LPS, structure, core, gene, isolate, microbiology, strain, polysaccharide, cell, chain, molecule, Research, side chain, Escherichia, Escherichia coli, type, predominant, cluster, gene cluster, O-polysaccharide, O polysaccharide, spectrometry, Salmonella, core region, region, mass spectrometry, reduction, biochemistry, biophysics, hexose, Hexoses, homolog, inner core, lead, Magnetic Resonance Spectroscopy, medicine, modification, modified, nuclear, nuclear magnetic resonance, nuclear magnetic resonance spectroscopy, plasmid, resonance, Salmonella enterica, spectroscopy, surface

  NCBI PubMed ID: 12591884
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: cwhitfie@uoguelph.ca
  Institutions: Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada. Biophysics. Analytical Biochemistry, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany
  
   
  
  Escherichia coli K12
  CSDB ID 2079 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Trivial name: core oligosaccharide
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135818,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7

• Article ID: 81
  Frirdich E, Lindner B, Holst O, Whitfield C "Overexpression of the waaZ gene leads to modification of the structure of the inner core region of Escherichia coli lipopolysaccharide, truncation of the outer core, and reduction of the amount of O polysaccharide on the cell surface" - Journal of Bacteriology 185(5) (2003) 1659-1671
  

  The waa gene cluster is responsible for the biosynthesis of the lipopolysaccharide (LPS) core region in Escherichia coli and Salmonella: Homologs of the waaZ gene product are encoded by the waa gene clusters of Salmonella enterica and E. coli strains with the K-12 and R2 core types. Overexpression of WaaZ in E. coli and S. enterica led to a modified LPS structure showing core truncations and (where relevant) to a reduction in the amount of O-polysaccharide side chains. Mass spectrometry and nuclear magnetic resonance spectroscopy were used to determine the predominant LPS structures in an E. coli isolate with an R1 core (waaZ is lacking from the type R1 waa gene cluster) with a copy of the waaZ gene added on a plasmid. Novel truncated LPS structures, lacking up to 3 hexoses from the outer core, resulted from WaaZ overexpression. The truncated molecules also contained a KdoIII residue not normally found in the R1 core

  Lipopolysaccharide, biosynthesis, LPS, structure, core, gene, isolate, microbiology, strain, polysaccharide, cell, chain, molecule, Research, side chain, Escherichia, Escherichia coli, type, predominant, cluster, gene cluster, O-polysaccharide, O polysaccharide, spectrometry, Salmonella, core region, region, mass spectrometry, reduction, biochemistry, biophysics, hexose, Hexoses, homolog, inner core, lead, Magnetic Resonance Spectroscopy, medicine, modification, modified, nuclear, nuclear magnetic resonance, nuclear magnetic resonance spectroscopy, plasmid, resonance, Salmonella enterica, spectroscopy, surface

  NCBI PubMed ID: 12591884
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: cwhitfie@uoguelph.ca
  Institutions: Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada. Biophysics. Analytical Biochemistry, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany
  
   
  
  Escherichia coli R1
  CSDB ID 2188 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Trivial name: core oligosaccharide
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_151528,IEDB_190606,IEDB_2189047,IEDB_225177,IEDB_226811,IEDB_232584,IEDB_885823,IEDB_983931,SB_192,SB_7

• Article ID: 81
  Frirdich E, Lindner B, Holst O, Whitfield C "Overexpression of the waaZ gene leads to modification of the structure of the inner core region of Escherichia coli lipopolysaccharide, truncation of the outer core, and reduction of the amount of O polysaccharide on the cell surface" - Journal of Bacteriology 185(5) (2003) 1659-1671
  

  The waa gene cluster is responsible for the biosynthesis of the lipopolysaccharide (LPS) core region in Escherichia coli and Salmonella: Homologs of the waaZ gene product are encoded by the waa gene clusters of Salmonella enterica and E. coli strains with the K-12 and R2 core types. Overexpression of WaaZ in E. coli and S. enterica led to a modified LPS structure showing core truncations and (where relevant) to a reduction in the amount of O-polysaccharide side chains. Mass spectrometry and nuclear magnetic resonance spectroscopy were used to determine the predominant LPS structures in an E. coli isolate with an R1 core (waaZ is lacking from the type R1 waa gene cluster) with a copy of the waaZ gene added on a plasmid. Novel truncated LPS structures, lacking up to 3 hexoses from the outer core, resulted from WaaZ overexpression. The truncated molecules also contained a KdoIII residue not normally found in the R1 core

  Lipopolysaccharide, biosynthesis, LPS, structure, core, gene, isolate, microbiology, strain, polysaccharide, cell, chain, molecule, Research, side chain, Escherichia, Escherichia coli, type, predominant, cluster, gene cluster, O-polysaccharide, O polysaccharide, spectrometry, Salmonella, core region, region, mass spectrometry, reduction, biochemistry, biophysics, hexose, Hexoses, homolog, inner core, lead, Magnetic Resonance Spectroscopy, medicine, modification, modified, nuclear, nuclear magnetic resonance, nuclear magnetic resonance spectroscopy, plasmid, resonance, Salmonella enterica, spectroscopy, surface

  NCBI PubMed ID: 12591884
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: cwhitfie@uoguelph.ca
  Institutions: Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada. Biophysics. Analytical Biochemistry, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany
  
   
  
  Escherichia coli K12
  CSDB ID 2189 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Trivial name: core oligosaccharide
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135818,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7

• Article ID: 81
  Frirdich E, Lindner B, Holst O, Whitfield C "Overexpression of the waaZ gene leads to modification of the structure of the inner core region of Escherichia coli lipopolysaccharide, truncation of the outer core, and reduction of the amount of O polysaccharide on the cell surface" - Journal of Bacteriology 185(5) (2003) 1659-1671
  

  The waa gene cluster is responsible for the biosynthesis of the lipopolysaccharide (LPS) core region in Escherichia coli and Salmonella: Homologs of the waaZ gene product are encoded by the waa gene clusters of Salmonella enterica and E. coli strains with the K-12 and R2 core types. Overexpression of WaaZ in E. coli and S. enterica led to a modified LPS structure showing core truncations and (where relevant) to a reduction in the amount of O-polysaccharide side chains. Mass spectrometry and nuclear magnetic resonance spectroscopy were used to determine the predominant LPS structures in an E. coli isolate with an R1 core (waaZ is lacking from the type R1 waa gene cluster) with a copy of the waaZ gene added on a plasmid. Novel truncated LPS structures, lacking up to 3 hexoses from the outer core, resulted from WaaZ overexpression. The truncated molecules also contained a KdoIII residue not normally found in the R1 core

  Lipopolysaccharide, biosynthesis, LPS, structure, core, gene, isolate, microbiology, strain, polysaccharide, cell, chain, molecule, Research, side chain, Escherichia, Escherichia coli, type, predominant, cluster, gene cluster, O-polysaccharide, O polysaccharide, spectrometry, Salmonella, core region, region, mass spectrometry, reduction, biochemistry, biophysics, hexose, Hexoses, homolog, inner core, lead, Magnetic Resonance Spectroscopy, medicine, modification, modified, nuclear, nuclear magnetic resonance, nuclear magnetic resonance spectroscopy, plasmid, resonance, Salmonella enterica, spectroscopy, surface

  NCBI PubMed ID: 12591884
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: cwhitfie@uoguelph.ca
  Institutions: Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada. Biophysics. Analytical Biochemistry, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany
  
   
  
  Escherichia coli R1
  CSDB ID 2190 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130670,IEDB_133751,IEDB_140088,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192

• Article ID: 92
  Gamian A, Katzenellenbogen E, Romanowska E, Dabrowski U, Dabrowski J "Lipopolysaccharide core region of Hafnia alvei: Structure elucidation using chemical methods, gas chromatography-mass spectrometry, and NMR spectroscopy" - Carbohydrate Research 266 (1995) 221-228
  

  Sugar and methylation analysis with the use of gas chromatography-mass spectrometry and 1H NMR spectroscopy proved that the core oligosaccharides isolated from lipopolysaccharides of eight Hafnia alvei strains have the identical hexasaccharide skeleton. However, 1H, 31P heterocorrelated spectra showed that the phosphorylation pattern is not the same. The branched heptose for the ATCC 13337, 1187, 2, 1191, 1196, 1220, and 481L strains is phosphorylated as in the following formula, where P = -O-P(O)(O-)2 and P-PxXEtN = [-O-P(O)(O-)]2-O(CH2)2NH3+ [formula: see text] A different phosphorylation pattern was found for the 1211 strain, where the branched heptose residue is 6-substituted by a monophosphorylethanolamine group, ...→3(→7)(PxXEtN→6)-α-LD-Hepp-(1→3)..., where PxXEtN = -O-P(O)(O-)-O(CH2)2NH3+.

  Lipopolysaccharide, NMR, core oligosaccharide, Hafnia alvei

  NCBI PubMed ID: 7535188
  Publication DOI: 10.1016/0008-6215(94)00266-I
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: gamian@immuno.iitd.pan.wroc.pl
  Institutions: Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Wroclaw, Poland., Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Wroclaw, Poland
  Methods: gel filtration, 1H NMR, NMR-2D, methylation, GLC-MS, NMR, HF solvolysis, sugar analysis, 31P NMR
  
   
  
  Hafnia alvei, Hafnia alvei ATCC 13337
  CSDB ID 2093 (all data & tools)
• Article ID: 951
  Lugowski C, Jachymek W, Niedziela T, Romanowska A, Witkowska D, Romanowska E "Lipopolysaccharide core region of Hafnia alvei: Serological characterization" - FEMS Immunology and Medical Microbiology 10 (1995) 119-124
  

  Covalent glycoconjugates containing, as a ligand lipopolysaccharide core, oligosaccharides of Hafnia alvei standard strain ATCC13337 and R mutant 1 M were used to produce anti-H. alvei core antibodies. The sera obtained were tested in rocket immunoelectrophoresis, immunoblotting and ELISA using H. alvei lipopolysaccharides of various strains. The experiments were carried out to study the antigenic relationships between lipopolysaccharide core regions in the H. alvei genus.

  Lipopolysaccharide, LPS, core, characterization, lipopolysaccharide core, serological, serology, Hafnia alvei, core region, region, Hafnia

  NCBI PubMed ID: 7719279
  Journal NLM ID: 9315554
  Publisher: Elsevier
  Correspondence: lugowski@immuno.pan.wroc.pl
  Institutions: Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Czerska 12, 53-114 Wroclaw, Poland, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław
  
   
  
  Hafnia alvei ATCC 13337, Hafnia alvei PCM 1187, Hafnia alvei PCM 1211, Hafnia alvei PCM 1191, Hafnia alvei PCM 1192, Hafnia alvei PCM 1196, Hafnia alvei PCM 1200, Hafnia alvei PCM 1209, Hafnia alvei PCM 1220, Hafnia alvei 481-L
  CSDB ID 3178 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135394,IEDB_135818,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7

• Article ID: 198
  Vinogradov EV, Van der Drift K, Thomas-Oates JE, Meshkov S, Brade H, Holst O "The structures of the carbohydrate backbones of the lipopolysaccharides from Escherichia coli rough mutants F470 (R1 core type) and F576 (R2 core type)" - European Journal of Biochemistry 261(3) (1999) 629-639
  

  The lipopolysaccharides (LPS) from Escherichia coli rough mutant strains F470 (R1 core type) and F576 (R2 core type) were deacylated yielding in each case a mixture of oligosaccharides with one predominant product which was isolated using high-performance anion-exchange chromatography. In addition, one oligosaccharide present in minor quantities was isolated from LPS of E. coli strain F576 (R2 core type). The structures of the oligosaccharides were determined by chemical analyses and NMR spectroscopic experiments. Furthermore, de-O-acylated and dephosphorylated LPS preparations were investigated by fast-atom bombardment and collision induced dissociation tandem mass spectrometry. The combined data allow us to deduce the following carbohydrate backbones of the E. coli R1 and R2 core types which share the following structure (Scheme 1 [see formula in text], but differ in the substituents R1 and R2 which for the R1 core type are predominantly: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]a-Glc-(1→3)-a-Glc-, R2 = H and to a minor extent: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]-a-Glc-(1→3)-a-Glc-, R2 = a-GlcN and for the R2 core type predominantly: R1 = a-GlcNAc-(1→2)-a-Glc-(1→2)-a-Glc-(1→3)-[a-Gal-(1→6)]-a-Glc-, R2 = H and to a minor extent: R1 = a-GlcNAc-[b-Gal-(1→4)]-(1→2)-a-Glc-(1→2)-a-Glc-[a-Gal-(1→6)]-(1→3)-a-Glc-, R2 = H in which all sugars are d-pyranoses (L,D-Hep, L-glycero-D-manno-heptopyranose; P, phosphate).

  Escherichia coli; lipopolysaccharide; core types R1 and R2; structural analysis

  NCBI PubMed ID: 10215878
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: oholst@fz-borstel.de
  Institutions: Center for Medicine and Biosciences, Borstel Research Center, Germany, Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands, Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR-2D, NMR, chemical analysis, MS
  
   
  
  Escherichia coli F470
  CSDB ID 5529 (all data & tools)
• Article ID: 3365
  Müller-Loennies S, Brade L, Brade H "Neutralizing and cross-reactive antibodies against enterobacterial lipopolysaccharide" - International Journal of Medical Microbiology 297(5) (2007) 321-340
  

  Lipopolysaccharide (LPS, endotoxin) elicits an immune reaction which is responsible for many of the harmful effects seen in septic shock patients. The eradication of bacteria by antibiotics is insufficient to resolve the pathology due to the lack of LPS neutralization. LPS-neutralizing antibodies have been described; however, these were specific for the serotype of the infecting bacteria and thus not useful for the treatment of septic shock patients. Structural analyses revealed that the LPS structures of Escherichia coli and Salmonella are structurally conserved in the inner core region. Using whole LPS and a panel of neoglycoconjugates containing purified LPS oligosaccharides, which we have obtained from all E. coli core types (K-12, R1, R2, R3 and R4), Salmonella enterica, and the mutant strain E. coli J-5, we have identified an epitope which is bound with high affinity by the monoclonal antibody WN1 222-5, which has been shown previously shown to be cross-reactive against a large collection of blood,fecal, and urinary isolates of E. coli, S. enterica, some Citrobacter, independently of the serotype [Di Padova, F.E., Brade, H., Barclay, G.R., Poxton, I.R., Liehl, E., Schuetze, E., Kocher, H.P., Ramsay, G., Schreier, M.H., McClelland, D.B., Rietschel, E.T., 1993. A broadly cross-protective monoclonal antibody binding to Escherichia coli and Salmonella lipopolysaccharides. Infect. Immun. 61, 3863-3872]. Importantly, WN1 222-5 was protective in various models of endotoxic shock. The minimal structural element necessary for high-affinity binding consists of R(1)-α-D-Glcp-(1→3)-[L-α-D-Hepp-(1→7)]-L-α-D-Hepp4P-(1→3)-R(2) (R(1), R(2)=additional sugars of LPS) in which the side-chain heptose and the 4-phosphate on the branched heptose are the main determinants of the epitope. Additional sugars of the outer core (R(1)) enhance the affinity, whereas loss of an intact Kdo region and/or lipid A (R(2)) prevent binding. The identification of the epitope provides the structural basis for the rational development of a potential vaccine against E. coli LPS

  Lipopolysaccharide, core, antibody, epitope, sepsis, therapy

  NCBI PubMed ID: 17544324
  Publication DOI: 10.1016/j.ijmm.2007.04.002
  Journal NLM ID: 100898849
  Publisher: Jena, Germany: Urban & Fischer Verlag
  Correspondence: sml@fz-borstel.de
  Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
  Methods: chemical analysis, serological methods
  
   
  
  Escherichia coli R1
  CSDB ID 21500 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135394,IEDB_135818,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7

• Article ID: 198
  Vinogradov EV, Van der Drift K, Thomas-Oates JE, Meshkov S, Brade H, Holst O "The structures of the carbohydrate backbones of the lipopolysaccharides from Escherichia coli rough mutants F470 (R1 core type) and F576 (R2 core type)" - European Journal of Biochemistry 261(3) (1999) 629-639
  

  The lipopolysaccharides (LPS) from Escherichia coli rough mutant strains F470 (R1 core type) and F576 (R2 core type) were deacylated yielding in each case a mixture of oligosaccharides with one predominant product which was isolated using high-performance anion-exchange chromatography. In addition, one oligosaccharide present in minor quantities was isolated from LPS of E. coli strain F576 (R2 core type). The structures of the oligosaccharides were determined by chemical analyses and NMR spectroscopic experiments. Furthermore, de-O-acylated and dephosphorylated LPS preparations were investigated by fast-atom bombardment and collision induced dissociation tandem mass spectrometry. The combined data allow us to deduce the following carbohydrate backbones of the E. coli R1 and R2 core types which share the following structure (Scheme 1 [see formula in text], but differ in the substituents R1 and R2 which for the R1 core type are predominantly: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]a-Glc-(1→3)-a-Glc-, R2 = H and to a minor extent: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]-a-Glc-(1→3)-a-Glc-, R2 = a-GlcN and for the R2 core type predominantly: R1 = a-GlcNAc-(1→2)-a-Glc-(1→2)-a-Glc-(1→3)-[a-Gal-(1→6)]-a-Glc-, R2 = H and to a minor extent: R1 = a-GlcNAc-[b-Gal-(1→4)]-(1→2)-a-Glc-(1→2)-a-Glc-[a-Gal-(1→6)]-(1→3)-a-Glc-, R2 = H in which all sugars are d-pyranoses (L,D-Hep, L-glycero-D-manno-heptopyranose; P, phosphate).

  Escherichia coli; lipopolysaccharide; core types R1 and R2; structural analysis

  NCBI PubMed ID: 10215878
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: oholst@fz-borstel.de
  Institutions: Center for Medicine and Biosciences, Borstel Research Center, Germany, Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands, Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR-2D, NMR, chemical analysis, MS
  
   
  
  Escherichia coli F470
  CSDB ID 5695 (all data & tools)
• Article ID: 3365
  Müller-Loennies S, Brade L, Brade H "Neutralizing and cross-reactive antibodies against enterobacterial lipopolysaccharide" - International Journal of Medical Microbiology 297(5) (2007) 321-340
  

  Lipopolysaccharide (LPS, endotoxin) elicits an immune reaction which is responsible for many of the harmful effects seen in septic shock patients. The eradication of bacteria by antibiotics is insufficient to resolve the pathology due to the lack of LPS neutralization. LPS-neutralizing antibodies have been described; however, these were specific for the serotype of the infecting bacteria and thus not useful for the treatment of septic shock patients. Structural analyses revealed that the LPS structures of Escherichia coli and Salmonella are structurally conserved in the inner core region. Using whole LPS and a panel of neoglycoconjugates containing purified LPS oligosaccharides, which we have obtained from all E. coli core types (K-12, R1, R2, R3 and R4), Salmonella enterica, and the mutant strain E. coli J-5, we have identified an epitope which is bound with high affinity by the monoclonal antibody WN1 222-5, which has been shown previously shown to be cross-reactive against a large collection of blood,fecal, and urinary isolates of E. coli, S. enterica, some Citrobacter, independently of the serotype [Di Padova, F.E., Brade, H., Barclay, G.R., Poxton, I.R., Liehl, E., Schuetze, E., Kocher, H.P., Ramsay, G., Schreier, M.H., McClelland, D.B., Rietschel, E.T., 1993. A broadly cross-protective monoclonal antibody binding to Escherichia coli and Salmonella lipopolysaccharides. Infect. Immun. 61, 3863-3872]. Importantly, WN1 222-5 was protective in various models of endotoxic shock. The minimal structural element necessary for high-affinity binding consists of R(1)-α-D-Glcp-(1→3)-[L-α-D-Hepp-(1→7)]-L-α-D-Hepp4P-(1→3)-R(2) (R(1), R(2)=additional sugars of LPS) in which the side-chain heptose and the 4-phosphate on the branched heptose are the main determinants of the epitope. Additional sugars of the outer core (R(1)) enhance the affinity, whereas loss of an intact Kdo region and/or lipid A (R(2)) prevent binding. The identification of the epitope provides the structural basis for the rational development of a potential vaccine against E. coli LPS

  Lipopolysaccharide, core, antibody, epitope, sepsis, therapy

  NCBI PubMed ID: 17544324
  Publication DOI: 10.1016/j.ijmm.2007.04.002
  Journal NLM ID: 100898849
  Publisher: Jena, Germany: Urban & Fischer Verlag
  Correspondence: sml@fz-borstel.de
  Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
  Methods: chemical analysis, serological methods
  
   
  
  Escherichia coli R1
  CSDB ID 21842 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_135394,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 198
  Vinogradov EV, Van der Drift K, Thomas-Oates JE, Meshkov S, Brade H, Holst O "The structures of the carbohydrate backbones of the lipopolysaccharides from Escherichia coli rough mutants F470 (R1 core type) and F576 (R2 core type)" - European Journal of Biochemistry 261(3) (1999) 629-639
  

  The lipopolysaccharides (LPS) from Escherichia coli rough mutant strains F470 (R1 core type) and F576 (R2 core type) were deacylated yielding in each case a mixture of oligosaccharides with one predominant product which was isolated using high-performance anion-exchange chromatography. In addition, one oligosaccharide present in minor quantities was isolated from LPS of E. coli strain F576 (R2 core type). The structures of the oligosaccharides were determined by chemical analyses and NMR spectroscopic experiments. Furthermore, de-O-acylated and dephosphorylated LPS preparations were investigated by fast-atom bombardment and collision induced dissociation tandem mass spectrometry. The combined data allow us to deduce the following carbohydrate backbones of the E. coli R1 and R2 core types which share the following structure (Scheme 1 [see formula in text], but differ in the substituents R1 and R2 which for the R1 core type are predominantly: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]a-Glc-(1→3)-a-Glc-, R2 = H and to a minor extent: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]-a-Glc-(1→3)-a-Glc-, R2 = a-GlcN and for the R2 core type predominantly: R1 = a-GlcNAc-(1→2)-a-Glc-(1→2)-a-Glc-(1→3)-[a-Gal-(1→6)]-a-Glc-, R2 = H and to a minor extent: R1 = a-GlcNAc-[b-Gal-(1→4)]-(1→2)-a-Glc-(1→2)-a-Glc-[a-Gal-(1→6)]-(1→3)-a-Glc-, R2 = H in which all sugars are d-pyranoses (L,D-Hep, L-glycero-D-manno-heptopyranose; P, phosphate).

  Escherichia coli; lipopolysaccharide; core types R1 and R2; structural analysis

  NCBI PubMed ID: 10215878
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: oholst@fz-borstel.de
  Institutions: Center for Medicine and Biosciences, Borstel Research Center, Germany, Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands, Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR-2D, NMR, chemical analysis, MS
  
   
  
  Escherichia coli F576
  CSDB ID 5696 (all data & tools)
• Article ID: 4303
  Gomery K, Müller-Loennies S, Brooks CL, Brade L, Kosma P, Di Padova F, Brade H, Evans SV "Antibody WN1 222-5 mimics Toll-like receptor 4 binding in the recognition of LPS" - Proceedings of the National Academy of Sciences of the USA 109(51) (2012) 20877-20882
  

  Escherichia coli infections, a leading cause of septic shock, remain a major threat to human health because of the fatal action to endotoxin (LPS). Therapeutic attempts to neutralize endotoxin currently focus on inhibiting the interaction of the toxic component lipid A with myeloid differentiating factor 2, which forms a trimeric complex together with Toll-like receptor 4 to induce immune cell activation. The 1.73-A resolution structure of the unique endotoxin-neutralizing protective antibody WN1 222-5 in complex with the core region shows that it recognizes LPS of all E. coli serovars in a manner similar to Toll-like receptor 4, revealing that protection can be achieved by targeting the inner core of LPS and that recognition of lipid A is not required. Such interference with Toll-like receptor complex formation opens new paths for antibody sepsis therapy independent of lipid A antagonists.

  structure, Escherichia coli, antibody, recognition, binding, Toll-like receptor 4

  NCBI PubMed ID: 23184990
  Publication DOI: 10.1073/pnas.1209253109
  Journal NLM ID: 7505876
  Publisher: National Academy of Sciences
  Correspondence: sml@fz-borstel.de; svevans@uvic.ca
  Institutions: Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8P 3P6, Research Center Borstel, Leibniz Center for Medicine and Biosciences, Medical and Biochemical Microbiology, D-23845 Borstel, Germany, Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G 2H7, Department of Chemistry, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
  Methods: ELISA, serological methods, crystallization
  
   
  
  Escherichia coli F576
  CSDB ID 27162 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_135394,IEDB_136044,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_232584,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88

• Article ID: 198
  Vinogradov EV, Van der Drift K, Thomas-Oates JE, Meshkov S, Brade H, Holst O "The structures of the carbohydrate backbones of the lipopolysaccharides from Escherichia coli rough mutants F470 (R1 core type) and F576 (R2 core type)" - European Journal of Biochemistry 261(3) (1999) 629-639
  

  The lipopolysaccharides (LPS) from Escherichia coli rough mutant strains F470 (R1 core type) and F576 (R2 core type) were deacylated yielding in each case a mixture of oligosaccharides with one predominant product which was isolated using high-performance anion-exchange chromatography. In addition, one oligosaccharide present in minor quantities was isolated from LPS of E. coli strain F576 (R2 core type). The structures of the oligosaccharides were determined by chemical analyses and NMR spectroscopic experiments. Furthermore, de-O-acylated and dephosphorylated LPS preparations were investigated by fast-atom bombardment and collision induced dissociation tandem mass spectrometry. The combined data allow us to deduce the following carbohydrate backbones of the E. coli R1 and R2 core types which share the following structure (Scheme 1 [see formula in text], but differ in the substituents R1 and R2 which for the R1 core type are predominantly: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]a-Glc-(1→3)-a-Glc-, R2 = H and to a minor extent: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]-a-Glc-(1→3)-a-Glc-, R2 = a-GlcN and for the R2 core type predominantly: R1 = a-GlcNAc-(1→2)-a-Glc-(1→2)-a-Glc-(1→3)-[a-Gal-(1→6)]-a-Glc-, R2 = H and to a minor extent: R1 = a-GlcNAc-[b-Gal-(1→4)]-(1→2)-a-Glc-(1→2)-a-Glc-[a-Gal-(1→6)]-(1→3)-a-Glc-, R2 = H in which all sugars are d-pyranoses (L,D-Hep, L-glycero-D-manno-heptopyranose; P, phosphate).

  Escherichia coli; lipopolysaccharide; core types R1 and R2; structural analysis

  NCBI PubMed ID: 10215878
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: oholst@fz-borstel.de
  Institutions: Center for Medicine and Biosciences, Borstel Research Center, Germany, Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands, Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR-2D, NMR, chemical analysis, MS
  
   
  
  Escherichia coli F576
  CSDB ID 5697 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130656,IEDB_130659,IEDB_130670,IEDB_130693,IEDB_130701,IEDB_133751,IEDB_135513,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_153307,IEDB_190606,IEDB_2189047,IEDB_225177,IEDB_226811,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_7,SB_72

• Article ID: 265
  Inagaki M, Kawaura T, Wakashima H, Kato M, Nishikawa S, Kashimura N "Different contributions of the outer and inner R-core residues of lipopolysaccharide to the recognition by spike H and G proteins of bacteriophage phiX174" - FEMS Microbiology Letters 226(2) (2003) 221-227
  

  The binding of spike H and G proteins of bacteriophage phiX174 with lipopolysaccharides (LPSs) were evaluated by a competitive enzyme-linked plate assay using the biotin-labeled LPS of Escherichia coli C, one of a host strain, and the non-labeled LPSs having different R-core polysaccharide lengths. H protein promptly decreased its affinity when some saccharide residues were truncated from the outer R-core. However, G protein showed significant affinity to the LPSs lacking all the residues of the outer R-core and some of the inner R-core. Thus, G protein rather than H protein well recognized the residues of the inner R-core of LPS

  LPS, core, bacteriophage, proteins, G-protein, phiX174, host recognition, spike protein

  NCBI PubMed ID: 14553915
  Journal NLM ID: 7705721
  Publisher: Blackwell Publishing
  Correspondence: inagaki@bio.mie-u.ac.jp
  Institutions: Department of Life Science, Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, 514-8507, Mie, Japan
  Methods: DOC-PAGE, enzyme-linked plate assay
  
   
  
  Salmonella enterica Typhimurium
  CSDB ID 7141 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 265
  Inagaki M, Kawaura T, Wakashima H, Kato M, Nishikawa S, Kashimura N "Different contributions of the outer and inner R-core residues of lipopolysaccharide to the recognition by spike H and G proteins of bacteriophage phiX174" - FEMS Microbiology Letters 226(2) (2003) 221-227
  

  The binding of spike H and G proteins of bacteriophage phiX174 with lipopolysaccharides (LPSs) were evaluated by a competitive enzyme-linked plate assay using the biotin-labeled LPS of Escherichia coli C, one of a host strain, and the non-labeled LPSs having different R-core polysaccharide lengths. H protein promptly decreased its affinity when some saccharide residues were truncated from the outer R-core. However, G protein showed significant affinity to the LPSs lacking all the residues of the outer R-core and some of the inner R-core. Thus, G protein rather than H protein well recognized the residues of the inner R-core of LPS

  LPS, core, bacteriophage, proteins, G-protein, phiX174, host recognition, spike protein

  NCBI PubMed ID: 14553915
  Journal NLM ID: 7705721
  Publisher: Blackwell Publishing
  Correspondence: inagaki@bio.mie-u.ac.jp
  Institutions: Department of Life Science, Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, 514-8507, Mie, Japan
  Methods: DOC-PAGE, enzyme-linked plate assay
  
   
  
  Escherichia coli O111:B4
  CSDB ID 7206 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135818,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7

• Article ID: 265
  Inagaki M, Kawaura T, Wakashima H, Kato M, Nishikawa S, Kashimura N "Different contributions of the outer and inner R-core residues of lipopolysaccharide to the recognition by spike H and G proteins of bacteriophage phiX174" - FEMS Microbiology Letters 226(2) (2003) 221-227
  

  The binding of spike H and G proteins of bacteriophage phiX174 with lipopolysaccharides (LPSs) were evaluated by a competitive enzyme-linked plate assay using the biotin-labeled LPS of Escherichia coli C, one of a host strain, and the non-labeled LPSs having different R-core polysaccharide lengths. H protein promptly decreased its affinity when some saccharide residues were truncated from the outer R-core. However, G protein showed significant affinity to the LPSs lacking all the residues of the outer R-core and some of the inner R-core. Thus, G protein rather than H protein well recognized the residues of the inner R-core of LPS

  LPS, core, bacteriophage, proteins, G-protein, phiX174, host recognition, spike protein

  NCBI PubMed ID: 14553915
  Journal NLM ID: 7705721
  Publisher: Blackwell Publishing
  Correspondence: inagaki@bio.mie-u.ac.jp
  Institutions: Department of Life Science, Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, 514-8507, Mie, Japan
  Methods: DOC-PAGE, enzyme-linked plate assay
  
   
  
  Escherichia coli C
  CSDB ID 7207 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130656,IEDB_130659,IEDB_130670,IEDB_130693,IEDB_133751,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7

• Article ID: 265
  Inagaki M, Kawaura T, Wakashima H, Kato M, Nishikawa S, Kashimura N "Different contributions of the outer and inner R-core residues of lipopolysaccharide to the recognition by spike H and G proteins of bacteriophage phiX174" - FEMS Microbiology Letters 226(2) (2003) 221-227
  

  The binding of spike H and G proteins of bacteriophage phiX174 with lipopolysaccharides (LPSs) were evaluated by a competitive enzyme-linked plate assay using the biotin-labeled LPS of Escherichia coli C, one of a host strain, and the non-labeled LPSs having different R-core polysaccharide lengths. H protein promptly decreased its affinity when some saccharide residues were truncated from the outer R-core. However, G protein showed significant affinity to the LPSs lacking all the residues of the outer R-core and some of the inner R-core. Thus, G protein rather than H protein well recognized the residues of the inner R-core of LPS

  LPS, core, bacteriophage, proteins, G-protein, phiX174, host recognition, spike protein

  NCBI PubMed ID: 14553915
  Journal NLM ID: 7705721
  Publisher: Blackwell Publishing
  Correspondence: inagaki@bio.mie-u.ac.jp
  Institutions: Department of Life Science, Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, 514-8507, Mie, Japan
  Methods: DOC-PAGE, enzyme-linked plate assay
  
   
  
  Salmonella enterica Typhimurium TV119
  CSDB ID 7208 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: (->6) lipid A
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_130693,IEDB_133751,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 265
  Inagaki M, Kawaura T, Wakashima H, Kato M, Nishikawa S, Kashimura N "Different contributions of the outer and inner R-core residues of lipopolysaccharide to the recognition by spike H and G proteins of bacteriophage phiX174" - FEMS Microbiology Letters 226(2) (2003) 221-227
  

  The binding of spike H and G proteins of bacteriophage phiX174 with lipopolysaccharides (LPSs) were evaluated by a competitive enzyme-linked plate assay using the biotin-labeled LPS of Escherichia coli C, one of a host strain, and the non-labeled LPSs having different R-core polysaccharide lengths. H protein promptly decreased its affinity when some saccharide residues were truncated from the outer R-core. However, G protein showed significant affinity to the LPSs lacking all the residues of the outer R-core and some of the inner R-core. Thus, G protein rather than H protein well recognized the residues of the inner R-core of LPS

  LPS, core, bacteriophage, proteins, G-protein, phiX174, host recognition, spike protein

  NCBI PubMed ID: 14553915
  Journal NLM ID: 7705721
  Publisher: Blackwell Publishing
  Correspondence: inagaki@bio.mie-u.ac.jp
  Institutions: Department of Life Science, Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, 514-8507, Mie, Japan
  Methods: DOC-PAGE, enzyme-linked plate assay
  
   
  
  Escherichia coli EH100
  CSDB ID 7209 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192

• Article ID: 265
  Inagaki M, Kawaura T, Wakashima H, Kato M, Nishikawa S, Kashimura N "Different contributions of the outer and inner R-core residues of lipopolysaccharide to the recognition by spike H and G proteins of bacteriophage phiX174" - FEMS Microbiology Letters 226(2) (2003) 221-227
  

  The binding of spike H and G proteins of bacteriophage phiX174 with lipopolysaccharides (LPSs) were evaluated by a competitive enzyme-linked plate assay using the biotin-labeled LPS of Escherichia coli C, one of a host strain, and the non-labeled LPSs having different R-core polysaccharide lengths. H protein promptly decreased its affinity when some saccharide residues were truncated from the outer R-core. However, G protein showed significant affinity to the LPSs lacking all the residues of the outer R-core and some of the inner R-core. Thus, G protein rather than H protein well recognized the residues of the inner R-core of LPS

  LPS, core, bacteriophage, proteins, G-protein, phiX174, host recognition, spike protein

  NCBI PubMed ID: 14553915
  Journal NLM ID: 7705721
  Publisher: Blackwell Publishing
  Correspondence: inagaki@bio.mie-u.ac.jp
  Institutions: Department of Life Science, Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, 514-8507, Mie, Japan
  Methods: DOC-PAGE, enzyme-linked plate assay
  
   
  
  Escherichia coli J5
  CSDB ID 7211 (all data & tools)