Show legend Show as text

Structure type: oligomer
Trivial name: core-lipid A carbohydrate backbone
Compound class: core oligosaccharide, LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_141807,IEDB_150908,IEDB_151531

• Article ID: 197
  Vinogradov EV, Petersen BO, Thomas-Oates JE, Duus JO, Brade H, Holst O "Characterization of a novel branched tetrasaccharide of 3-deoxy-D-manno-oct-2-ulopyranosonic acid. The structure of the carbohydrate backbone of the lipopolyasccharide from Acinetobacter baumannii strain NCTC 10303 (ATCC 17904)" - Journal of Biological Chemistry 273(43) (1998) 28122-28131
  

  For the first time, the tetrasaccharide Kdo a2→5 Kdo a2→5 (Kdo a2→4)Kdo (Kdo is 3-deoxy-Dmanno-oct-2-ulopyranosonic acid) has been identified in a bacterial lipopolysaccharide (LPS), i.e. in the core region of LPS from Acinetobacter baumannii NCTC 10303. The LPS was analyzed using compositional analysis, mass spectrometry, and NMR spectroscopy. The disaccharide DGlcpN b1→6 DGlcpN, phosphorylated at O-1 and O-4', was identified as the carbohydrate backbone of the lipid A. The Kdo tetrasaccharide is attached to O-6' of this disaccharide and is further substituted by short L-rhamnoglycans of varying length and by the disaccharide DGlcpNAc a1→4 DGlcpNA (GlcpNA, 2-amino-2-deoxy-glucopyranosuronic acid). The core region is not substituted by phosphate residues and represents a novel core type of bacterial LPS. The complete carbohydrate backbone of the LPS is shown in Structure I as follows: [see formula in text] where Rha is rhamnose. Except were indicated, monosaccharides possess the D-configuration. Sugars marked with an asterisk are present in non-stoichiometric amounts.

  LPS, structure, core, acid, Acinetobacter, Acinetobacter baumannii, 3-deoxy-D-manno-oct-2-ulopyranosonic

  NCBI PubMed ID: 9774431
  Publication DOI: 10.1074/jbc.273.43.28122
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: oholst@fz-borstel.de
  Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany, Department of Chemistry, Carlsberg Laboratory, DK-2500 Valby, Denmark, Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University,NL-3584 CA Utrecht, The Netherlands
  Methods: NMR-2D, NMR, MS, composition analysis
  
   
  
  Acinetobacter baumannii NCTC 10303
  CSDB ID 5691 (all data & tools)
• Article ID: 806
  Heine H, Müller-Loennies S, Brade L, Lindner B, Brade H "Endotoxic activity and chemical structure of lipopolysaccharides from Chlamydia trachomatis serotypes E and L2 and Chlamydophila psittaci 6BC" - European Journal of Biochemistry 270(3) (2003) 440-450
  

  The lipopolysaccharide (LPS) of Chlamydia trachomatis serotype E was isolated from tissue culture-grown elementary bodies and analyzed structurally by mass spectrometry and 1H, 13C and 31P nuclear magnetic resonance. The LPS is composed of the same pentasaccharide bisphosphate αKdo-(2-8)-αKdo-(2-4)-αKdo-(2-6)-βGlcN-4P-(1-6) αGlcN-1P (Kdo is 3-deoxy-α-D-manno-oct-2-ulosonic acid) as reported for C. trachomatis serotype L2[Rund, S., Lindner, B., Brade, H. and Holst, O. (1999) J. Biol. Chem. 274, 16819-16824]. The glucosamine disaccharide backbone is substituted with a complex mixture of fatty acids with ester or amide linkage whereby no ester-linked hydroxy fatty acids were found. The LPS was purified carefully (with contaminations by protein or nucleic acids below 0.3%) and tested for its ability to induce proinflammatory cytokines in several readout systems in comparison to LPS from C. trachomatis serotype L2 and Chlamydophila psittaci strain 6BC as well as enterobacterial smooth and rough LPS and synthetic hexaacyl lipid A. The chlamydial LPS were at least 10 times less active than typical endotoxins; specificity of the activities was confirmed by inhibition with the LPS antagonist, B1233, or with monoclonal antibodies against chlamydial LPS. Like other LPS, the chlamydial LPS used toll-like receptor TLR4 for signalling, but unlike other LPS activation was strictly CD14-dependent.

  LPS, Chlamydia, Chlamydia trachomatis, Chlamydophila psittaci, MALDI-TOF MS, toll-like receptors, innate immunity, ESI-FTIR-MS, ESI-FT-IR MS

  NCBI PubMed ID: 12542694
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: hbrade@fz-borstel.de
  Institutions: Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany
  Methods: HPAEC
  
   
  
  Chlamydia trachomatis E
  CSDB ID 2541 (all data & tools)
• Article ID: 814
  Holst O, Bock K, Brade L, Brade H "The structures of oligosaccharide bisphosphates isolated from the lipopolysaccharide of a recombinant Escherichia coli strain expressing the gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] of Chlamydia psittaci 6BC" - European Journal of Biochemistry 229 (1995) 194-200
  

  The lipopolysaccharide from the recombinant strain Escherichia coli F515-140 containing the cloned gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] from Chlamydia psittaci 6BC was isolated and sequentially de-O-acylated and de-N-acylated. The products were separated by high-performance anion-exchange chromatography into three fractions, two of which contained a single compound. Their structures were elucidated by high-field NMR spectroscopy as α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 1) (tetrasaccharide bisphosphate) [Holst, O., Broer, W., Thomas-Oates, J. E., Mamat, U. & Brade, H. (1993) Eur. J. Biochem. 214, 703-710] and α-Kdo-(2→4)-[α-Kdo-(2→8)-]-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 4) (hexasaccharide bisphosphate). The third fraction comprised two pentasaccharide bisphosphates, which could be separated by affinity chromatography using an immobilized monoclonal antibody specific for the trisaccharide α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo. The bound fraction was identified as α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 2) [Holst, O., Broer, W., Thomas-Oates, J. E., Mamat, U. & Brade, H. (1993) Eur. J. Biochem. 214, 703-710], whereas the unbound fraction was identified as α-Kdo-(2→4)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 3). This novel Kdo tetrasaccharide extends our knowledge on multifunctional Kdo transferases.

  Lipopolysaccharide, LPS, oligosaccharide, structure, core, gene, strain, Escherichia, Escherichia coli, acid, Kdo, transferase, phosphate, Chlamydia, recombinant, bisphosphate, Chlamydia psittaci, gseA, HPLC

  NCBI PubMed ID: 7744029
  Publication DOI: 10.1111/j.1432-1033.1995.0194l.x
  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: Division of Biochemical Microbiology, Forschungsinstitut Borstel, Germany, Division of Biochemical Microbiology, Institut fur Experimentelle Biologie und Medizin, Forschungsinstitut Borstel, Germany, Department of Chemistry, Carisberg Laboratory, Copenhagen, Denmark
  Methods: 13C NMR, 1H NMR, GLC-MS, 31P NMR, HPAEC, affinity chromatography
  
   
  
  Escherichia coli F515-140
  CSDB ID 2426 (all data & tools)
• Article ID: 1157
  Rund S, Lindner B, Brade H, Holst O "Structural analysis of the lipopolysaccharide from Chlamydophila psittaci strain 6BC" - European Journal of Biochemistry 267(18) (2000) 5717-5726
  

  The lipopolysaccaride of Chlamydophila psittaci 6BC was isolated from tissue culture-grown elementary bodies using a modified phenol/water procedure followed by extraction with phenol/chloroform/light petroleum. Compositional analyses indicated the presence of 3-deoxy-Dmanno-oct-2-ulosonic acid, GlcN, organic bound phosphate and fatty acids in a molar ratio of approximately 3. 3 : 2 : 1.8 : 4.6. Deacylated lipopolysaccharide was obtained after successive microscale treatment with hydrazine and potassium hydroxide, and was then separated by high performance anion-exchange chromatography into two major fractions, the structures of which were determined by 600 MHz NMR spectroscopy as α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcpN-(1→6)-α-D-GlcpN 1,4'-bisphosphate and α-Kdo-(2→4)-[α-Kdo-(2→8)]-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcpN-(1→6)-α-D-GlcpN 1,4'-bisphosphate. The distribution of fatty acids in lipid A was determined by compositional analyses andmatrix-assisted laser desorption/ionization time-of-flight mass spectrometry experiments on lipid A and de-O-acylated lipid A. It was shown that the carbohydrate backbone of lipid A is replaced by a complex mixture of fatty acids, including long-chain and branched (R)-configured 3-hydroxy fatty acids, the latter being exclusively present in an amide linkage

  Lipopolysaccharide, strain, structural, serotype, analysis, structural analysis, Chlamydophila psittaci, NMR spectroscopy, mass spectrometry

  NCBI PubMed ID: 10971582
  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: Divisions of Medical and Biochemical Microbiology and Biophysics, Research Center Borstel, Center for Medicine and Biosciences, Germany
  Methods: 13C NMR, 1H NMR, NMR-2D, MALDI-TOF MS
  
   
  
  Chlamydophila psittaci 6BC
  CSDB ID 4475 (all data & tools)
• Article ID: 1386
  Brabetz W, Lindner B, Brade H "Comparative analyses of secondary gene products of 3-deoxy-D-manno-oct-2-ulosonic acid transferases from Chlamydiaceae in Escherichia coli K-12" - European Journal of Biochemistry 267(17) (2000) 5458-5465
  

  The waaA gene encoding the essential, lipopolysaccharide (LPS)-specific 3-deoxy-Dmanno-oct-2-ulosonic acid (Kdo) transferase was inactivated in the chromosome of a heptosyltransferase I and II deficient Escherichia coli K-12 strain by insertion of gene expression cassettes encoding the waaA genes of Chlamydia trachomatis, Chlamydophila pneumoniae or Chlamydophila psittaci. The three chlamydial Kdo transferases were able to complement the knockout mutation without changing the growth or multiplication behaviour. The LPS of the mutants were serologically and structurally characterized in comparison to the LPS of the parent strain using compositional analyses, high performance anion exchange chromatography, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and specific monoclonal antibodies. The data show that chlamydial Kdo transferases can replace in E. coli K-12 the host's Kdo transferase and retain the product specificities described in their natural background. In addition, we unequivocally proved that WaaA from C. psittaci transfers predominantly four Kdo residues to lipid A, forming a branched tetrasaccharide with the structure α-Kdo-(2→8)-[α-Kdo-(2→4)]-α-Kdo-(2→4)-α-Kdo.

  Lipopolysaccharide, LPS, gene, Escherichia, Escherichia coli, 3-deoxy-D-manno-oct-2-ulosonic acid, acid, Kdo, transferase, transferases, Chlamydiaceae, genetic complementation, multifunctional 3-deoxy-D-manno-oct-2, product specificity, ulosonic acid transferases

  NCBI PubMed ID: 10951204
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: wbrabetz@fz-borstel.de
  Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Divizion of Medical and Biochemical Microbiology, Research Centre Borstel, Centre for Medicine and Biosciences,Borstel,Germany
  
   
  
  Chlamydia trachomatis L2, Chlamydophila pneumoniae TW-183, Escherichia coli K12 (WBB51), Escherichia coli K12 (WBB52), Escherichia coli K12 (WBB53)
  CSDB ID 6419 (all data & tools)
• Article ID: 1387
  Brabetz W, Müller-Loennies S, Holst O, Brade H "Deletion of the heptosyl transferase genes rfaC and rfaF in Escherichia coli K-12 results in an Re-type lipopolysaccharide with a high degree of 2-aminoethyl phosphate substitution" - European Journal of Biochemistry 247 (1997) 716-724
  

  The chromosomal genes rfaC and rfaF of Escherichia coli W3110 were inactivated by allelic-replacement mutagenesis to generate a defined strain lacking both heptosyltransferases which catalyze in lipopolysaccharide (LPS) biosynthesis the transfer of the first two L-glycero-D-manno-heptose (Hep) residues to 3-deoxy-D-manno-2-octulosonic acid (Kdo). The LPS of the mutant was isolated and its chemical structure was investigated by compositional analysis and nuclear magnetic resonance spectroscopy of isolated, deacylated oligosaccharide phosphates. The basic structure was a tetrasaccharide α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN4P-(1→6)-α-D-GlcN1P which in LPS was substituted at position 07 of Kdo II by 2-aminoethanol phosphate in non-stoichiometric amounts. 2-Aminoethanol was cleaved during deacylation of the LPS by successive hydrazinolysis and KOH treatment and, in addition, phosphate migration from 07 to 08 of Kdo II occurred. Thus, the oligosaccharides α-Kdo7P-(2→4)-α-Kdo-(2→6)-β-D-GlcN4P-(1→6)-α-D-GlcN1P and α-Kdo8P-(2→4)-α-Kdo-(2→6)-β-D-GlcN4P-(1→6)-α-D-GlcN1P could be isolated. KOH treatment of the two trisphosphates and authentic methyl 3-deoxy-D-manno-octulopyranoside 7-(2-acetamidoethyl phosphate) proved that phosphate migration only took place when the phosphate group was substituted with 2-aminoethanol. Complementation studies with plasmid-encoded rfaC and rfaF genes revealed that the mutant strain can be used in combination with LPS-specific antibodies for the cloning and characterization of heptosytransferases which glycosylate Kdo residues of the inner core region of LPS.

  Lipopolysaccharide, heptosyltransferase, phosphate migration, Escherichia coli K-12, Re mutant, rfaC

  NCBI PubMed ID: 9266718
  Publication DOI: 10.1111/j.1432-1033.1997.00716.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany
  Methods: NMR, HPAEC
  
   
  
  Escherichia coli K12 (Re-mutant)
  CSDB ID 6372 (all data & tools)
• Article ID: 2446
  Holst O, Broer W, Thomas-Oates JE, Mamat U, Brade H "Structural analysis of two oligosaccharide biphosphates isolated from the lipopolysaccharide of a recombinant strain of Escherichia coli F515 (Re chemotype) expressing the genus-specific epitope of Chlamydia lipopolysaccharide" - European Journal of Biochemistry 214(3) (1993) 703-710
  

  The lipopolysaccharide of the recombinant strain Escherichia coli F515-207, expressing the genus-specific epitope of Chlamydia lipopolysaccharide, was sequentially de-O- and de-N-acylated by mild hydrazinolysis and treatment with 4 M KOH, respectively, yielding two oligosaccharide bisphosphates which were isolated by high-performance anion-exchange chromatography and gel-permeation chromatography. Their structures were determined by chemical analysis, NMR spectroscopy, and mass spectrometry as α-Kdo-(2-4)-α-Kdo-(2-6)-β-D-GlcN-(1-6)-α-D-GlcN 1,4'-P2 (tetrasaccharide bisphosphate) and α-Kdo-(2-8)-α-Kdo-(2-4)-α-Kdo-(2-6)-β-D-GlcN-(1-6)-α- D-GlcN 1,4'-P2 (pentasaccharide bisphosphate).

  NCBI PubMed ID: 7686488
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Division of Biochemical Microbiology, Forschungsinstitut Borstel, Germany
  
   
  
  Escherichia coli F515-207
  CSDB ID 124180 (all data & tools)
• Article ID: 3825
  Brooks CL, Müller-Loennies S, Borisova SN, Brade L, Kosma P, Hirama T, MacKenzie CR, Brade H, Evans SV "Antibodies raised against chlamydial lipopolysaccharide antigens reveal convergence in germline gene usage and differential epitope recognition" - Biochemistry 49(3) (2010) 570-581
  

  The structures of antigen-binding fragments from two related monoclonal antibodies have been determined to high resolution in the presence of several carbohydrate antigens raised against chlamydial lipopolysaccharide. With the exception of CDR H3, antibodies S54-10 and S73-2 are both derived from the same set of germline gene segments as the previously reported structures S25-2 and S45-18. Despite this similarity, the antibodies differ in specificity and the mechanism by which they recognize their cognate antigen. S54-10 uses an unrelated CDR H3 to recognize its antigen in a fashion analogous to S45-18; however, S73-2 recognizes the same antigen as S45-18 and S54-10 in a wholly unrelated manner. Together, these antibody-antigen structures provide snapshots into how the immune system uses the same set of inherited germline gene segments to generate multiple possible specificities that allow for differential recognition of epitopes and how unrelated CDR H3 sequences can result in convergent binding of clinically relevant bacterial antigens.

  antibodies, epitope, recognition, antigens, Chlamydia, binding

  NCBI PubMed ID: 20000757
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Correspondence: hebra@fz-borstel.de; svevans@uvic.ca
  Institutions: University of Victoria, Department of Biochemistry and Microbiology, PO Box 3055 STN CSC, Victoria, BC, Canada V8P 3P6
  Methods: ELISA, serological methods, genetic methods, crystallization, surface plasmon resonance (SPR)
  
   
  
  Chlamydia
  CSDB ID 25552 (all data & tools)
• Article ID: 4895
  Kenyon JJ, Duda KA, De Felice A, Cunneen MM, Molinaro A, Laitinen J, Skurnik M, Holst O, Reeves PR, De Castro C "Serotype O:8 isolates in the Yersinia pseudotuberculosis complex have different O-antigen gene clusters and produce various forms of rough LPS" - Innate Immunity 22(3) (2016) 205-217
  

  In Yersinia pseudotuberculosis complex, the O-antigen of LPS is used for the serological characterization of strains, and 21 serotypes have been identified to date. The O-antigen biosynthesis gene cluster and corresponding O-antigen structure have been described for 18, leaving O:8, O:13 and O:14 unresolved. In this study, two O:8 isolates were examined. The O-antigen gene cluster sequence of strain 151 was near identical to serotype O:4a, though a frame-shift mutation was found in ddhD, while No. 6 was different to 151 and carried the O:1b gene cluster. Structural analysis revealed that No. 6 produced a deeply truncated LPS, suggesting a mutation within the waaF gene. Both ddhD and waaF were cloned and expressed in 151 and No. 6 strains, respectively, and it appeared that expression of ddhD gene in strain 151 restored the O-antigen on LPS, while waaF in No. 6 resulted in an LPS truncated less severely but still without the O-antigen, suggesting that other mutations occurred in this strain. Thus, both O:8 isolates were found to be spontaneous O-antigen-negative mutants derived from other validated serotypes, and we propose to remove this serotype from the O-serotyping scheme, as the O:8 serological specificity is not based on the O-antigen.

  O-antigen, O-specific polysaccharide, Yersinia pseudotuberculosis, serotyping, O-antigen gene cluster, O-antigen biosynthesis, O:8 serotype

  NCBI PubMed ID: 26873504
  Publication DOI: 10.1177/1753425916631403
  Journal NLM ID: 101469670
  Publisher: Sage Publications
  Correspondence: decastro@unina.it
  Institutions: Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany, Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland, Department of Chemical Sciences, University of Napoli, Napoli, Italy, Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland, School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia, Department of Agriculture Sciences, University of Napoli, Portici, Italy
  Methods: 13C NMR, 1H NMR, NMR-2D, PCR, SDS-PAGE, DNA techniques, ESI-MS, DOC-PAGE, Western blotting, composition analysis, NMR-1D, genetic methods, GPC, de-N-acylation, hydrazinolysis, function analysis of gene clusters, ESI-IT-TOF-MS/MS
  
   
  
  Yersinia pseudotuberculosis O8
  CSDB ID 11630 (all data & tools)