Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141582,IEDB_141584,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_153207,IEDB_885822,IEDB_983931,SB_192

• Article ID: 800
  Datta AK, Basu S, Roy N "Chemical and immunochemical studies of the O-antigen from enteropathogenic Escherichia coli O158 lipopolysaccharide" - Carbohydrate Research 322(3-4) (1999) 219-227
  

  The O-specific polysaccharide isolated from Escherichia coli O158 smooth lipopolysaccharide contains L-rhamnose, D-glucose and 2-acetamido-2-deoxy-D-galactose in the molar ratios 1:2:2. Studies on composition, methylation analysis and specific degradations together with a 1H and 13C NMR spectral study established that the O-antigen is built up from a pentasaccharide repeating unit having the following structure: (see struc. in text). The most effective inhibitory part of the oligosaccharide from E. coli O158 lipopolysaccharide has been serologically characterized by an ELISA-inhibition study using different sugars. The results showed that methyl a- and b-D-GalpNAc are the most effective inhibitors among the monosaccharides tested, while the main antibody specificity lies on the main-chain trisaccharide repeating unit.

  Lipopolysaccharide, structure, O-antigen, O antigen, Escherichia, Escherichia coli, chemical, immunochemical, enteropathogenic, inhibition ELISA

  NCBI PubMed ID: 10637986
  Publication DOI: 10.1016/S0008-6215(99)00199-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Biological Chemistry, Indian Association for the Cultivation of Sciences, Calcutta, India
  Methods: methylation, partial acid hydrolysis, sugar analysis, Smith degradation
  
   
  
  Escherichia coli O158
  CSDB ID 1351 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: Rb2 core
Contained glycoepitopes: IEDB_130693,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_983931,SB_192

• Article ID: 963
  Mansfield LP, Forsythe SJ "Demonstration of the Rb1 lipopolysaccharide core structure in Salmonella strains with the monoclonal antibody M105" - Journal of Medical Microbiology 50(4) (2001) 339-344
  

  The lipopolysaccharide (LPS) from 42 strains representing 19 Salmonella serogroups was differentiated into characteristic ladder-like profiles by SDS-PAGE analysis. The core-specific antibody M105 (Ra, Rb1 and Rb2) was used in an immunoblot assay of SDS-PAGE-separated LPS molecules. The M105 antibody bound to the R-type LPS of 18 of the 20 Salmonella strains tested. The results demonstrate that S. enterica serotype Godesberg, S. Adelaide (one of two strains), S. Milwaukee, S. Niarembe, S. Bere and S. Arizonae (serogroup 63) have an atypical LPS core structure which is Rb1 type.

  structure, monoclonal antibodies, lipopolysaccharide core, Salmonella, strains

  NCBI PubMed ID: 11289519
  Publication DOI: 10.1099/0022-1317-50-4-339
  Journal NLM ID: 0224131
  Publisher: Reading, England: Society for General Microbiology
  Correspondence: Thomas.Hartung@unikonstanz.de
  Institutions: University of Konstanz, Biochemical Pharmacology, Konstanz, Germany
  
   
  
  Salmonella enterica
  CSDB ID 3401 (all data & tools)

Show legend Show as text

Structure type: oligomer ; 2486.59
Trivial name: core-lipid A carbohydrate backbone
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135394,IEDB_135818,IEDB_136044,IEDB_136095,IEDB_136906,IEDB_137472,IEDB_140088,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_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88

• Article ID: 1029
  Müller-Loennies S, Lindner B, Brade H "Structural analysis of deacylated lipopolysaccharide of Escherichia coli strains 2513 (R4 core-type) and F653 (R3 core-type)" - European Journal of Biochemistry 269(23) (2002) 5982-5991
  

  Lipopolysaccharide (LPS) of Escherichia coli strain 2513 (R4 core-type) yielded after alkaline deacylation one major oligosaccharide by high- performance anion-exchange chromatography (HPAEC) which had a molecular mass of 2486.59 Da as determined by electrospray ionization mass spectrometry. This was in accordance with the calculated molecular mass of a tetraphosphorylated dodecasaccharide of the composition shown below. NMR-analyses identified the chemical structure as where L-α-D-Hep is L-glycero-α-D-manno-heptopyranose and Kdo is 3-deoxy-α-D-manno-oct-2-ulopyranosylonic acid and all hexoses are present as d- pyranoses. We have also isolated the complete core-oligosaccharides of E. coli F653 LPS for which only preliminary data were available and investigated the deacylated LPS by NMR and MS/ The proposal structure determined previously by methylation analysis was confirmed and is shown below. In additional we have quantified the side-chain heptose substitution of the inner core with GlcpN (~30%) and confirmed that this sugar is only present when the phosphate at the second LDHep residue is absent.

  Lipopolysaccharide, LPS, oligosaccharide, structure, core, strain, structural, analysis, molecular, Escherichia, Escherichia coli, acid, Kdo, core oligosaccharide, high, electrospray, ionization mass spectrometry, spectrometry, structural analysis, chemical, chemical structure, mass spectrometry, hexose, Hexoses, alkaline, ionization, composition, molecular mass, deacylated, deacylation, chromatography, pyranose, anion-exchange, anion-exchange chromatography, Electrospray Ionization, electrospray-ionization, HPAEC, R3 core-type, R4 core-type

  NCBI PubMed ID: 12444988
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: sml@fz-borstel.de
  Institutions: Borstel Research Center, Center for Medicine and Biosciences, Borstel, Germany.
  Methods: NMR, ESI-MS, HPAEC
  
   
  
  Escherichia coli 2513
  CSDB ID 3723 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: O-deacetylated lipid A
Compound class: LPS
Contained glycoepitopes: 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_885823,IEDB_983931,SB_192,SB_7

• Article ID: 1038
  Müller-Loennies S, Lindner B, Brade H "Structural analysis of oligosaccharides from lipopolysaccharide (LPS) of Escherichia coli K12 strain W3100 reveals a link between inner and outer core LPS biosynthesis" - Journal of Biological Chemistry 278(36) (2003) 34090-34101
  

  Lipopolysaccharide (LPS) from Escherichia coli K12 W3100 is known to contain several glycoforms, and the basic structure has been investigated previously by methylation analyses (Holst, O. (1999) in Endotoxin in Health and Disease (Brade, H., Opal, S. M., Vogel, S. N., and Morrison, D., eds) pp. 115-154; Marcel Dekker, Inc., New York). In order to reveal dependences of gene activity and LPS structure, we have now determined the composition of de-O-acylated LPS by electrospray ionization-Fourier transform ion cyclotron-mass spectrometry (ESI-FT-MS) and identified 11 different LPS molecules. We have isolated the major glycoforms after de-O- and de-N-acylation and obtained four oligosaccharides that differed in their carbohydrate structure and phosphate substitution. The main oligosaccharide accounted for approximately 70% of the total and had a molecular mass of 2516 Da according to ESI-FT-MS. The dodecasaccharide structure (glycoform I) as determined by NMR was consistent with MS and compositional analysis. One minor oligosaccharide (5%) of the same carbohydrate structure did not contain the 4'-phosphate of the lipid A. Two oligosaccharides contained the same phosphate substitution but differed in their carbohydrate structure, one (5%) which contained an additional β-D-GlcN in 1→7 linkage on a terminal heptose residue (glycoform II) which was N-acetylated in LPS. A minor amount of a molecule lacking the terminal L-α-D-Hep in the outer core but otherwise identical to the major oligosaccharide (glycoform III) could only be identified by ESI-FT-MS of the de-O-acylated LPS. The other oligosaccharide (20%) contained an α-Kdo-(2→4)-[α-L-Rha-(1→5)]-α-Kdo-(2→4)-α-Kdo branched tetrasaccharide connected to the lipid A (glycoform IV). This novel inner core structure was accompanied by a truncation of the outer core in which the terminal disaccharide L-α-D-Hep-(1→6)-α-D-Glc was missing. The latter structure was identified for the first time in LPS and revealed that changes in the inner core structure may be accompanied by structural changes in the outer core.

  Lipopolysaccharide, biosynthesis, LPS, oligosaccharide, core, strain, structural, analysis, Escherichia, Escherichia coli, Oligosaccharides, structural analysis

  NCBI PubMed ID: 12819207
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: sml@fz-borstel.de
  Institutions: Borstel Research Center, Center for Medicine and Biosciences, Borstel, Germany
  Methods: NMR, ESI-MS, IRMPD-MS
  
   
  
  Escherichia coli K12 W3100
  CSDB ID 3738 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_137777,IEDB_137779,IEDB_138949,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_2189047,IEDB_983931,SB_192

• Article ID: 1048
  Nesper J, Kraiss A, Schild S, Blabeta J, Klose KE, Bockemuhl J, Reidl J "Comparative and genetic analyses of the putative Vibrio cholerae lipopolysaccharide core oligosaccharide biosynthesis (wav) gene cluster" - Infection and Immunity 70(5) (2002) 2419-2433
  

  We identified five different putative wav gene cluster types, which are responsible for the synthesis of the core oligosaccharide (OS) region of Vibrio cholerae lipopolysaccharide. Preliminary evidence that the genes encoded by this cluster are involved in core OS biosynthesis came from analysis of the recently released O1 El Tor V. cholerae genome sequence and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of O1 El Tor mutant strains defective in three genes (waaF, waaL, and wavB). Investigations of 38 different V. cholerae strains by Southern blotting, PCR, and sequencing analyses showed that the O1 El Tor wav gene cluster type is prevalent among clinical isolates of different serogroups associated with cholera and environmental O1 strains. In contrast, we found differences in the wav gene contents of 19 unrelated non-O1, non-O139 environmental and human isolates not associated with cholera. These strains contained four new wav gene cluster types that differ from each other in distinct gene loci, providing evidence for horizontal transfer of wav genes and for limited structural diversity of the core OS among V. cholerae isolates. Our results show genetic diversity in the core OS biosynthesis gene cluster and predominance of the type 1 wav gene locus in strains associated with clinical cholera, suggesting that a specific core OS structure could contribute to V. cholerae virulence

  Lipopolysaccharide, biosynthesis, genetic, synthesis, transfer, LPS, oligosaccharide, structure, core, blotting, clinical, gene, human, isolate, PCR, strain, structural, virulence, analysis, locus, type, core oligosaccharide, lipopolysaccharide core, lipopolysaccharide core oligosaccharide, cluster, gene cluster, specific, mutant, serogroup, putative, region, sequencing, sequence, difference, Vibrio, content, Vibrio cholerae, genome, gel electrophoresis, cholera, genetic diversity, diversity, electrophoresis, gel, environmental

  NCBI PubMed ID: 11953379
  Journal NLM ID: 0246127
  Publisher: American Society for Microbiology
  Correspondence: oachim.reidl@mail.uni-wuerzburg.de
  Institutions: Zentrum fur Infektionsforschung, Universitat Wurzburg, Wurzburg, Germany, Hygiene Institut Hamburg, Hamburg, Germany. University of Texas Health Science Center, San Antonio, Texas 78284-7758
  Methods: genetic methods
  
   
  
  Vibrio cholerae O1, Vibrio cholerae O139, Vibrio cholerae O22
  CSDB ID 3759 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: core-lipid A backbone
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135394,IEDB_135818,IEDB_136044,IEDB_136095,IEDB_136906,IEDB_137472,IEDB_140088,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_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88

• Article ID: 1029
  Müller-Loennies S, Lindner B, Brade H "Structural analysis of deacylated lipopolysaccharide of Escherichia coli strains 2513 (R4 core-type) and F653 (R3 core-type)" - European Journal of Biochemistry 269(23) (2002) 5982-5991
  

  Lipopolysaccharide (LPS) of Escherichia coli strain 2513 (R4 core-type) yielded after alkaline deacylation one major oligosaccharide by high- performance anion-exchange chromatography (HPAEC) which had a molecular mass of 2486.59 Da as determined by electrospray ionization mass spectrometry. This was in accordance with the calculated molecular mass of a tetraphosphorylated dodecasaccharide of the composition shown below. NMR-analyses identified the chemical structure as where L-α-D-Hep is L-glycero-α-D-manno-heptopyranose and Kdo is 3-deoxy-α-D-manno-oct-2-ulopyranosylonic acid and all hexoses are present as d- pyranoses. We have also isolated the complete core-oligosaccharides of E. coli F653 LPS for which only preliminary data were available and investigated the deacylated LPS by NMR and MS/ The proposal structure determined previously by methylation analysis was confirmed and is shown below. In additional we have quantified the side-chain heptose substitution of the inner core with GlcpN (~30%) and confirmed that this sugar is only present when the phosphate at the second LDHep residue is absent.

  Lipopolysaccharide, LPS, oligosaccharide, structure, core, strain, structural, analysis, molecular, Escherichia, Escherichia coli, acid, Kdo, core oligosaccharide, high, electrospray, ionization mass spectrometry, spectrometry, structural analysis, chemical, chemical structure, mass spectrometry, hexose, Hexoses, alkaline, ionization, composition, molecular mass, deacylated, deacylation, chromatography, pyranose, anion-exchange, anion-exchange chromatography, Electrospray Ionization, electrospray-ionization, HPAEC, R3 core-type, R4 core-type

  NCBI PubMed ID: 12444988
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: sml@fz-borstel.de
  Institutions: Borstel Research Center, Center for Medicine and Biosciences, Borstel, Germany.
  Methods: NMR, ESI-MS, HPAEC
  
   
  
  Escherichia coli F635
  CSDB ID 3805 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: core-lipid A backbone
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_135394,IEDB_135818,IEDB_136044,IEDB_136095,IEDB_136906,IEDB_137472,IEDB_140088,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_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88

• Article ID: 1029
  Müller-Loennies S, Lindner B, Brade H "Structural analysis of deacylated lipopolysaccharide of Escherichia coli strains 2513 (R4 core-type) and F653 (R3 core-type)" - European Journal of Biochemistry 269(23) (2002) 5982-5991
  

  Lipopolysaccharide (LPS) of Escherichia coli strain 2513 (R4 core-type) yielded after alkaline deacylation one major oligosaccharide by high- performance anion-exchange chromatography (HPAEC) which had a molecular mass of 2486.59 Da as determined by electrospray ionization mass spectrometry. This was in accordance with the calculated molecular mass of a tetraphosphorylated dodecasaccharide of the composition shown below. NMR-analyses identified the chemical structure as where L-α-D-Hep is L-glycero-α-D-manno-heptopyranose and Kdo is 3-deoxy-α-D-manno-oct-2-ulopyranosylonic acid and all hexoses are present as d- pyranoses. We have also isolated the complete core-oligosaccharides of E. coli F653 LPS for which only preliminary data were available and investigated the deacylated LPS by NMR and MS/ The proposal structure determined previously by methylation analysis was confirmed and is shown below. In additional we have quantified the side-chain heptose substitution of the inner core with GlcpN (~30%) and confirmed that this sugar is only present when the phosphate at the second LDHep residue is absent.

  Lipopolysaccharide, LPS, oligosaccharide, structure, core, strain, structural, analysis, molecular, Escherichia, Escherichia coli, acid, Kdo, core oligosaccharide, high, electrospray, ionization mass spectrometry, spectrometry, structural analysis, chemical, chemical structure, mass spectrometry, hexose, Hexoses, alkaline, ionization, composition, molecular mass, deacylated, deacylation, chromatography, pyranose, anion-exchange, anion-exchange chromatography, Electrospray Ionization, electrospray-ionization, HPAEC, R3 core-type, R4 core-type

  NCBI PubMed ID: 12444988
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: sml@fz-borstel.de
  Institutions: Borstel Research Center, Center for Medicine and Biosciences, Borstel, Germany.
  Methods: NMR, ESI-MS, HPAEC
  
   
  
  Escherichia coli F635
  CSDB ID 3900 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: core-lipid A carbohydrate backbone
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_135394,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192

• Article ID: 1037
  Müller-Loennies S, Brade L, MacKenzie CR, Di Padova FE, Brade H "Identification of a cross-reactive epitope widely present in lipopolysaccharide from enterobacteria and recognized by the cross-protective monoclonal antibody WN1 222-5" - Journal of Biological Chemistry 278(28) (2003) 25618-25627
  

  Septic shock due to infections with Gram-negative bacteria is a severe disease with a high mortality rate. We report the identification of the antigenic determinants of an epitope that is present in enterobacterial lipopolysaccharide (LPS) and recognized by a cross-reactive monoclonal antibody (mAb WN1 222-5) regarded as a potential means of treatment. Using whole LPS and a panel of neoglycoconjugates containing purified LPS oligosaccharides obtained from Escherichia coli core types R1, R2, R3, and R4, Salmonella enterica, and the mutant strain E. coli J-5, we showed that mAb WN1 222-5 binds to the distal part of the inner core region and recognizes the structural element R1-α-D-Glcp-(1→3)-[L-α-D-Hepp-(1→7)]-L-α-D-Hepp 4P-(1→3)-R2 (where R1 represents additional sugars of the outer core and R2 represents additional sugars of the inner core), which is common to LPS from all E. coli, Salmonella, and Shigella. WN1 222-5 binds poorly to molecules that lack the side chain heptose or lack phosphate at the branched heptose. Also molecules that are substituted with GlcpN at the side chain heptose are poorly bound. Thus, the side chain heptose and the 4-phosphate on the branched heptose are main determinants of the epitope. We have determined the binding kinetics and affinities (KD values) of the monovalent interaction of E. coli core oligosaccharides with WN1 222-5 by surface plasmon resonance and isothermal titration microcalorimetry. Affinity constants (KD values) determined by SPR were in the range of 3.6 x 10-5 to 3.2 x 10-8 m, with the highest affinity being observed for the core oligosaccharide from E. coli F576 (R2 core type) and the lowest KD values for those from E. coli J-5. Affinities of E. coli R1, R3, and R4 oligosaccharides were 5-10-fold lower, and values from the E. coli J-5 mutant were 29-fold lower than the R2 core oligosaccharide. Thus, the outer core sugars had a positive effect on binding

  Lipopolysaccharide, lipopolysaccharides, LPS, oligosaccharide, branched, common, core, heptose, chemistry, disease, metabolism, potential, strain, structural, Support, Non-U.S.Gov't, antigenic determinant, chain, molecule, Research, side chain, Escherichia, Escherichia coli, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, phosphate, Oligosaccharides, type, Carbohydrate Sequence, core oligosaccharide, high, infection, Molecular Sequence Data, epitopes, MAb, bacteria, mutant, Salmonella, enterobacterial, sugar, identification, core region, region, inner core, Magnetic Resonance Spectroscopy, medicine, resonance, Salmonella enterica, surface, enterobacteria, Shigella, interaction, Gram-negative bacteria, gram negative bacteria, Gram-negative, mutation, treatment, purified, sugars, antigenic, determinant, binding, bound, effect, Enterobacteriaceae, cross-reactive, heptoses, enzyme-linked immunosorbent assay, constant, neoglycoconjugate, affinity, calorimetry, cross-protective, Dose-Response Relationship, Immunologic, kinetics, mortality, plasmon, Protein Binding, septic, septic shock, shock, Surface Plasmon Resonance, Time Factors, titration

  NCBI PubMed ID: 12716894
  Publication DOI: 10.1074/jbc.M302904200
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: sml@fz-borstel.de
  Institutions: Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Institute for Biological Sciences, national research Council of Canada, Ottava, Ontario, K1A 0R6, Canada, Novartis Pharma AG, CH-4002 Base, Switzerland
  Methods: NMR, serological methods
  
   
  
  Escherichia coli J5
  CSDB ID 3818 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: lipid A
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_136044,IEDB_136095,IEDB_137472,IEDB_137777,IEDB_137779,IEDB_138949,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88

• Article ID: 1048
  Nesper J, Kraiss A, Schild S, Blabeta J, Klose KE, Bockemuhl J, Reidl J "Comparative and genetic analyses of the putative Vibrio cholerae lipopolysaccharide core oligosaccharide biosynthesis (wav) gene cluster" - Infection and Immunity 70(5) (2002) 2419-2433
  

  We identified five different putative wav gene cluster types, which are responsible for the synthesis of the core oligosaccharide (OS) region of Vibrio cholerae lipopolysaccharide. Preliminary evidence that the genes encoded by this cluster are involved in core OS biosynthesis came from analysis of the recently released O1 El Tor V. cholerae genome sequence and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of O1 El Tor mutant strains defective in three genes (waaF, waaL, and wavB). Investigations of 38 different V. cholerae strains by Southern blotting, PCR, and sequencing analyses showed that the O1 El Tor wav gene cluster type is prevalent among clinical isolates of different serogroups associated with cholera and environmental O1 strains. In contrast, we found differences in the wav gene contents of 19 unrelated non-O1, non-O139 environmental and human isolates not associated with cholera. These strains contained four new wav gene cluster types that differ from each other in distinct gene loci, providing evidence for horizontal transfer of wav genes and for limited structural diversity of the core OS among V. cholerae isolates. Our results show genetic diversity in the core OS biosynthesis gene cluster and predominance of the type 1 wav gene locus in strains associated with clinical cholera, suggesting that a specific core OS structure could contribute to V. cholerae virulence

  Lipopolysaccharide, biosynthesis, genetic, synthesis, transfer, LPS, oligosaccharide, structure, core, blotting, clinical, gene, human, isolate, PCR, strain, structural, virulence, analysis, locus, type, core oligosaccharide, lipopolysaccharide core, lipopolysaccharide core oligosaccharide, cluster, gene cluster, specific, mutant, serogroup, putative, region, sequencing, sequence, difference, Vibrio, content, Vibrio cholerae, genome, gel electrophoresis, cholera, genetic diversity, diversity, electrophoresis, gel, environmental

  NCBI PubMed ID: 11953379
  Journal NLM ID: 0246127
  Publisher: American Society for Microbiology
  Correspondence: oachim.reidl@mail.uni-wuerzburg.de
  Institutions: Zentrum fur Infektionsforschung, Universitat Wurzburg, Wurzburg, Germany, Hygiene Institut Hamburg, Hamburg, Germany. University of Texas Health Science Center, San Antonio, Texas 78284-7758
  Methods: genetic methods
  
   
  
  Vibrio cholerae non-O1, Vibrio cholerae non-O139, Vibrio cholerae H11
  CSDB ID 3843 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: O-deacetylated lipid A
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 1038
  Müller-Loennies S, Lindner B, Brade H "Structural analysis of oligosaccharides from lipopolysaccharide (LPS) of Escherichia coli K12 strain W3100 reveals a link between inner and outer core LPS biosynthesis" - Journal of Biological Chemistry 278(36) (2003) 34090-34101
  

  Lipopolysaccharide (LPS) from Escherichia coli K12 W3100 is known to contain several glycoforms, and the basic structure has been investigated previously by methylation analyses (Holst, O. (1999) in Endotoxin in Health and Disease (Brade, H., Opal, S. M., Vogel, S. N., and Morrison, D., eds) pp. 115-154; Marcel Dekker, Inc., New York). In order to reveal dependences of gene activity and LPS structure, we have now determined the composition of de-O-acylated LPS by electrospray ionization-Fourier transform ion cyclotron-mass spectrometry (ESI-FT-MS) and identified 11 different LPS molecules. We have isolated the major glycoforms after de-O- and de-N-acylation and obtained four oligosaccharides that differed in their carbohydrate structure and phosphate substitution. The main oligosaccharide accounted for approximately 70% of the total and had a molecular mass of 2516 Da according to ESI-FT-MS. The dodecasaccharide structure (glycoform I) as determined by NMR was consistent with MS and compositional analysis. One minor oligosaccharide (5%) of the same carbohydrate structure did not contain the 4'-phosphate of the lipid A. Two oligosaccharides contained the same phosphate substitution but differed in their carbohydrate structure, one (5%) which contained an additional β-D-GlcN in 1→7 linkage on a terminal heptose residue (glycoform II) which was N-acetylated in LPS. A minor amount of a molecule lacking the terminal L-α-D-Hep in the outer core but otherwise identical to the major oligosaccharide (glycoform III) could only be identified by ESI-FT-MS of the de-O-acylated LPS. The other oligosaccharide (20%) contained an α-Kdo-(2→4)-[α-L-Rha-(1→5)]-α-Kdo-(2→4)-α-Kdo branched tetrasaccharide connected to the lipid A (glycoform IV). This novel inner core structure was accompanied by a truncation of the outer core in which the terminal disaccharide L-α-D-Hep-(1→6)-α-D-Glc was missing. The latter structure was identified for the first time in LPS and revealed that changes in the inner core structure may be accompanied by structural changes in the outer core.

  Lipopolysaccharide, biosynthesis, LPS, oligosaccharide, core, strain, structural, analysis, Escherichia, Escherichia coli, Oligosaccharides, structural analysis

  NCBI PubMed ID: 12819207
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: sml@fz-borstel.de
  Institutions: Borstel Research Center, Center for Medicine and Biosciences, Borstel, Germany
  Methods: NMR, ESI-MS, IRMPD-MS
  
   
  
  Escherichia coli K12 W3100
  CSDB ID 3846 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: O-deacetylated lipid A
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 1038
  Müller-Loennies S, Lindner B, Brade H "Structural analysis of oligosaccharides from lipopolysaccharide (LPS) of Escherichia coli K12 strain W3100 reveals a link between inner and outer core LPS biosynthesis" - Journal of Biological Chemistry 278(36) (2003) 34090-34101
  

  Lipopolysaccharide (LPS) from Escherichia coli K12 W3100 is known to contain several glycoforms, and the basic structure has been investigated previously by methylation analyses (Holst, O. (1999) in Endotoxin in Health and Disease (Brade, H., Opal, S. M., Vogel, S. N., and Morrison, D., eds) pp. 115-154; Marcel Dekker, Inc., New York). In order to reveal dependences of gene activity and LPS structure, we have now determined the composition of de-O-acylated LPS by electrospray ionization-Fourier transform ion cyclotron-mass spectrometry (ESI-FT-MS) and identified 11 different LPS molecules. We have isolated the major glycoforms after de-O- and de-N-acylation and obtained four oligosaccharides that differed in their carbohydrate structure and phosphate substitution. The main oligosaccharide accounted for approximately 70% of the total and had a molecular mass of 2516 Da according to ESI-FT-MS. The dodecasaccharide structure (glycoform I) as determined by NMR was consistent with MS and compositional analysis. One minor oligosaccharide (5%) of the same carbohydrate structure did not contain the 4'-phosphate of the lipid A. Two oligosaccharides contained the same phosphate substitution but differed in their carbohydrate structure, one (5%) which contained an additional β-D-GlcN in 1→7 linkage on a terminal heptose residue (glycoform II) which was N-acetylated in LPS. A minor amount of a molecule lacking the terminal L-α-D-Hep in the outer core but otherwise identical to the major oligosaccharide (glycoform III) could only be identified by ESI-FT-MS of the de-O-acylated LPS. The other oligosaccharide (20%) contained an α-Kdo-(2→4)-[α-L-Rha-(1→5)]-α-Kdo-(2→4)-α-Kdo branched tetrasaccharide connected to the lipid A (glycoform IV). This novel inner core structure was accompanied by a truncation of the outer core in which the terminal disaccharide L-α-D-Hep-(1→6)-α-D-Glc was missing. The latter structure was identified for the first time in LPS and revealed that changes in the inner core structure may be accompanied by structural changes in the outer core.

  Lipopolysaccharide, biosynthesis, LPS, oligosaccharide, core, strain, structural, analysis, Escherichia, Escherichia coli, Oligosaccharides, structural analysis

  NCBI PubMed ID: 12819207
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: sml@fz-borstel.de
  Institutions: Borstel Research Center, Center for Medicine and Biosciences, Borstel, Germany
  Methods: NMR, ESI-MS, IRMPD-MS
  
   
  
  Escherichia coli K12 W3100
  CSDB ID 3847 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: O-deacetylated lipid A
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_135813,IEDB_136906,IEDB_137340,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: 1038
  Müller-Loennies S, Lindner B, Brade H "Structural analysis of oligosaccharides from lipopolysaccharide (LPS) of Escherichia coli K12 strain W3100 reveals a link between inner and outer core LPS biosynthesis" - Journal of Biological Chemistry 278(36) (2003) 34090-34101
  

  Lipopolysaccharide (LPS) from Escherichia coli K12 W3100 is known to contain several glycoforms, and the basic structure has been investigated previously by methylation analyses (Holst, O. (1999) in Endotoxin in Health and Disease (Brade, H., Opal, S. M., Vogel, S. N., and Morrison, D., eds) pp. 115-154; Marcel Dekker, Inc., New York). In order to reveal dependences of gene activity and LPS structure, we have now determined the composition of de-O-acylated LPS by electrospray ionization-Fourier transform ion cyclotron-mass spectrometry (ESI-FT-MS) and identified 11 different LPS molecules. We have isolated the major glycoforms after de-O- and de-N-acylation and obtained four oligosaccharides that differed in their carbohydrate structure and phosphate substitution. The main oligosaccharide accounted for approximately 70% of the total and had a molecular mass of 2516 Da according to ESI-FT-MS. The dodecasaccharide structure (glycoform I) as determined by NMR was consistent with MS and compositional analysis. One minor oligosaccharide (5%) of the same carbohydrate structure did not contain the 4'-phosphate of the lipid A. Two oligosaccharides contained the same phosphate substitution but differed in their carbohydrate structure, one (5%) which contained an additional β-D-GlcN in 1→7 linkage on a terminal heptose residue (glycoform II) which was N-acetylated in LPS. A minor amount of a molecule lacking the terminal L-α-D-Hep in the outer core but otherwise identical to the major oligosaccharide (glycoform III) could only be identified by ESI-FT-MS of the de-O-acylated LPS. The other oligosaccharide (20%) contained an α-Kdo-(2→4)-[α-L-Rha-(1→5)]-α-Kdo-(2→4)-α-Kdo branched tetrasaccharide connected to the lipid A (glycoform IV). This novel inner core structure was accompanied by a truncation of the outer core in which the terminal disaccharide L-α-D-Hep-(1→6)-α-D-Glc was missing. The latter structure was identified for the first time in LPS and revealed that changes in the inner core structure may be accompanied by structural changes in the outer core.

  Lipopolysaccharide, biosynthesis, LPS, oligosaccharide, core, strain, structural, analysis, Escherichia, Escherichia coli, Oligosaccharides, structural analysis

  NCBI PubMed ID: 12819207
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: sml@fz-borstel.de
  Institutions: Borstel Research Center, Center for Medicine and Biosciences, Borstel, Germany
  Methods: NMR, ESI-MS, IRMPD-MS
  
   
  
  Escherichia coli K12 W3100
  CSDB ID 3848 (all data & tools)

Show legend Show as text

Structure type: polymer biological repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_147450,IEDB_151531,IEDB_153217,IEDB_190606,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_23,SB_24,SB_7,SB_8,SB_88

• Article ID: 1135
  Ravenscroft N, Dabrowski J, Romanowska E "Structural elucidation of the biological repeating unit of O-specific polysaccharide from Citrobacter serotype O41" - European Journal of Biochemistry 229 (1995) 299-307
  

  Sugar analysis of the O-specific polysaccharide produced by Citrobacter serotype O41 revealed the presence of a hexasaccharide repeating unit, which includes the unusual 3-amino-N-(D-3'-hydroxybutyryl)-3,6-dideoxy-D-galactosyl residue (Fuc3NAcyl). The structure of the repeating unit was determined by extensive use of homo- and heteronuclear two-dimensional NMR spectroscopy, including the application of long-range 1H-13C correlation experiments and NOE studies to establish the sequence of sugar units. Indentification of the Glc β1→2 Fuc3NAcyl β1→6 GlcNAc α1→ sequence at the non-reducing terminus establishes the biological repeating unit of this O-specific polysaccharide as: →2 Glc β1→ Fuc3NAcyl β1→6 GlcNAc α1→ (Glc α1→2) 4Gal β1→3 GalNAc β1→. This structure is similar to that found for the O-specific polysaccharide isolated from Hafnia alvei strain 1211 [Katzenellenbogen, E., Romanowska, E., Dabrowski, U. & Dabrowski, J. (1991) Eur. J. Biochem. 200, 401-407], which differs in having an acetyl substituent at O4 of the Fuc3NAcyl residue and a branch point of GalNAc α substituted by Glc β at O3; these differences are responsible for the only weak serological cross-reactivity of the two strains.

  Lipopolysaccharide, 6-dideoxy-D-galactose, endotoxin, Citrobacter, 3-amino-N-(D-3'-hydroxybutyryl)-3

  NCBI PubMed ID: 7744044
  Publication DOI: 10.1111/j.1432-1033.1995.0299l.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Max-Planck-Institut fur Medizinische Forschung, Heidelberg, Germany
  Methods: 13C NMR, 1H NMR, methylation, periodate oxidation, NMR-2D
  
   
  
  Citrobacter sp. O41
  CSDB ID 4318 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_136017,IEDB_137473,IEDB_140630,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_153510,IEDB_423153,IEDB_733911,IEDB_983931,SB_192

• Article ID: 1240
  Sidorczyk Z, Zych K, Toukach FV, Arbatsky NP, Shashkov AS, Zablotni A, Knirel YA "Structure of the O-polysaccharide and classification of Proteus mirabilis strain G1 in Proteus serogroup O3" - European Journal of Biochemistry 269(5) (2002) 1406-1412
  

  The O-chain polysaccharide of the lipopolysaccharide (LPS) of a previously nonclassified strain of Proteus mirabilis termed G1 was studied by sugar analysis and 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, rotating-frame NOE (ROESY), H-detected 1H,13C HMQC, and heteronuclear multiple-bond correlation (HMBC) experiments. The following structure of the polysaccharide was established: [carbohydrate structure: see text] where D-GalA6(L-Lys) stands for N(α)-(D-galacturonoyl)-L-lysine. The structure of the O-polysaccharide of P. mirabilis G1 is similar, but not identical, to that of P. mirabilis S1959 and OXK belonging to serogroup O3. Immunochemical studies with P. mirabilis G1 and S1959 anti-(O-polysaccharide) sera revealed close LPS-based serological relatedness of P. mirabilis G1 and S1959, and therefore it was suggested to classify P. mirabilis G1 in serogroup O3 as a subgroup. P. mirabilis G1 and S1959 anti-(O-polysaccharide) sera also cross-reacted with LPS of P. mirabilis strains from two other serogroups containing D-GalA6(L-Lys) in the O-polysaccharide or in the core region.

  Lipopolysaccharide, O-polysaccharide, Proteus mirabilis, serogroup, N(α)-(D-galacturonoyl)-L-lysine

  NCBI PubMed ID: 11874454
  Publication DOI: 10.1046/j.1432-1033.2002.02782.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: zsidor@taxus.biol.uni.lodz.pl
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of General Microbiology, Institute of Microbiology and Immunology, University of Łodź, Łodź, Poland
  Methods: NMR
  
   
  
  Proteus mirabilis S1959 (O3)
  CSDB ID 4821 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_115013,IEDB_130645,IEDB_130695,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_138950,IEDB_141495,IEDB_141794,IEDB_141806,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_149558,IEDB_151528,IEDB_190606,IEDB_742249,IEDB_918314,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_87,SB_88

• Article ID: 1347
  Abeygunawardana C, Williams TC, Sumner JS, Hennessey JP "Development and validation of an NMR-based identity assay for bacterial polysaccharides" - Analytical Biochemistry 279(2) (2000) 226-240
  

  A method utilizing NMR spectroscopy has been developed to confirm the identity of bacterial polysaccharides used to formulate a polyvalent pneumococcal polysaccharide vaccine. The method is based on 600 MHz proton NMR spectra of individual serotype-specific polysaccharides. A portion of the anomeric region of each spectrum (5.89 to 4.64 ppm) is compared to spectra generated for designated reference samples for each polysaccharide of interest. The selected region offers a spectral window that is unique to a given polysaccharide and is sensitive to any structural alteration of the repeating units. The similarity of any two spectral profiles is evaluated using a correlation coefficient (rho), where rho >/= 0.95 between a sample and reference profile indicates a positive identification of the sample polysaccharide. This method has been shown to be extremely selective in its ability to discriminate between serotype-specific polysaccharides, some of which differ by no more than a single glycosidic linkage. Furthermore, the method is rapid and does not require extensive sample manipulations or pretreatments. The method was validated as a qualitative identity assay and will be incorporated into routine quality control testing of polysaccharide powders to be used in preparation of the polyvalent pneumococcal vaccine PNEUMOVAX 23. The specificity and reproducibility of the NMR-based identity assay is superior to the currently used colorimetric assays and can be readily adapted for use with other bacterial polysaccharide preparations as well.

  NMR, Bacterial, polysaccharide, Bacterial polysaccharide, polysaccharides, bacterial polysaccharides, assay, development, identity assay, method development, validation

  NCBI PubMed ID: 10706792
  Publication DOI: 10.1006/abio.1999.447
  Journal NLM ID: 0370535
  Publisher: Academic Press
  Correspondence: abey@merck.com
  Institutions: Bioprocess and Bioanalytical Research, Merck Research Laboratories, West Point, Pensylvania, USA
  Methods: NMR
  
   
  
  Streptococcus pneumoniae 11A
  CSDB ID 6404 (all data & tools)