Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_141794,IEDB_142488,IEDB_146664,IEDB_151528,IEDB_151770,IEDB_190606,IEDB_983931,SB_192,SB_7

• Article ID: 287
  Keller M, Roxlau A, Weng WM, Schmidt M, Quandt J, Niehaus K, Jording D, Arnold W, Puhler A "Molecular analysis of the Rhizobium meliloti mucR gene regulating the biosynthesis of the exopolysaccharides succinoglycan and galactoglucan" - Molecular Plant-Microbe Interactions 8 (1995) 267-277
  

  The Rhizobium meliloti Tn5 mutant Rm3131, producing galactoglucan (EPS II) instead of succinoglycan (EPS I), was complemented by a 3.6-kb EcoRI-fragment of the Rhizobium meliloti genome. Sequencing of this fragment revealed six open reading frames (ORFs). The ORF found to be affected in the mutant Rm3131 codes for a putative protein of 15.7 kDa and forms a monocistronic transcriptional unit. Further genetic analysis revealed that the gene mutated in Rm3131 is identical to the previously described R. meliloti mucR gene (H. Zhan, S.B. Levery, C. C. Lee, and J.A. Leigh, 1989, Proc. Natl. Acad. Sci. USA 86:3055-3059). By hybridization it was shown that a mucR homologous gene is present in several rhizobacteria. The deduced amino acid sequence of MucR showed nearly 80% identity to the Agrobacterium tumefaciens Ros protein, a negative regulator of vir genes and necessary for succinoglycan production. MucR contains like Ros a putative zinc finger sequence of the C2H2 type. Transcriptional fusions of genes for EPS I and EPS II synthesis, the so-called exo and exp genes, with the marker gene lacZ were used to delineate the role of mucR for exo and exp gene expression. It was found that exp genes are negatively regulated by MucR on the transcriptional level, whereas a posttranscriptional regulation by MucR is assumed for exo genes. Furthermore, mucR is negatively regulating its own transcription.

  symbiosis, exopolysaccharide synthesis, gene regulation

  NCBI PubMed ID: 7756693
  Publication DOI: 10.1094/MPMI-8-0267
  Journal NLM ID: 9107902
  Institutions: Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Federal Republic of Germany
  Methods: 13C NMR, DNA sequencing, DNA techniques, genetic methods, enzyme assay
  
   
  
  Rhizobium meliloti RmJQ46
  CSDB ID 31514 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_136105,IEDB_137472,IEDB_140630,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_190606,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983931,SB_192

• Article ID: 301
  Lee CH, Frasch CE "Quantification of bacterial polysaccharides by the purpald assay: Measurement of periodate-generated formaldehyde from glycol in the repeating unit" - Analytical Biochemistry 296(1) (2001) 73-82
  

  We have adapted the purpald assay for measurement of bacterial polysaccharides (PS) containing substituted and/or unsubstituted glycol (SG or UG) in residues such as glycerol, ribitol, arabinitol, furanosyl galactose, and sialyl. For the purpald assay of UG-containing PS, 50 microL of PS samples was consecutively reacted with 50 microL of 16 mM NaIO4 for 20 min, 50 microL of 136 mM purpald reagent in 2 N NaOH for 20 min, and 50 microL of 64 mM NaIO4 for 20 min in a 96-well tissue culture plate followed by a measurement of absorbance at 550 nm with a plate reader. For SG-containing PS, conversion of SG to UG with 25 micro;L of 0.3 N NaOH, 1 h at room temperature for de-O-acetylation followed by 25 microL of 0.6 M H2SO4, 1 h at 80 degrees C for acid hydrolysis of PS precedes the periodate treatment in the purpald assay. The concentration of the samples can be calculated from the sample absorbance and the reference standard curve constructed from the reference concentrations of the same PS (well-characterized) and their corresponding absorbance values assayed in the same plate. The purpald assay provides a tool in addition to the existing ones for the measurement of glycol-containing PS. Among the usefulness of this method are the determinations of the glycerol content in the phospho-glycerol-containing PS and the SG and UG contents and structural integrity in PS and conjugate vaccines.

  repeating unit, bacterial polysaccharides, quantification

  NCBI PubMed ID: 11520034
  Publication DOI: 10.1006/abio.2001.5230
  Journal NLM ID: 0370535
  Publisher: Academic Press
  Institutions: Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, OVRR, CBER, FDA, 8800 Rockville Pike, Bethesda, MD, USA
  Methods: purpald assay measurement
  
   
  
  Streptococcus pneumoniae 22F
  CSDB ID 7520 (all data & tools)
• 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 22F
  CSDB ID 6413 (all data & tools)
• Article ID: 4836
  Berti F, Ravenscroft N "Characterization of Carbohydrate Vaccines by NMR Spectroscopy" - Methods in Molecular Biology 1331 (2015) 189-209
  

  Physicochemical techniques are a powerful tool for the structural characterization of carbohydrate-based vaccines. High-field Nuclear Magnetic Resonance (NMR) spectroscopy has been established as an extremely useful and robust method for tracking the industrial manufacturing process of these vaccines from polysaccharide bulk antigen through to the final formulation. Here, we describe the use of proton NMR for structural identity and conformity testing of carbohydrate-based vaccines.

  carbohydrates, capsular polysaccharide, antigens, nuclear magnetic resonance spectroscopy, vaccines

  NCBI PubMed ID: 26169742
  Publication DOI: 10.1007/978-1-4939-2874-3_12
  Journal NLM ID: 9214969
  Publisher: Springer
  Correspondence: francesco.x.berti@gsk.com
  Institutions: Research, GSK Vaccines, Via Fiorentina 1, 53100, Siena, Italy
  
   
  
  Streptococcus pneumoniae 22F
  CSDB ID 11114 (all data & tools)
• Article ID: 5129
  Berti F, De Ricco R, Rappuoli R "Role of O-Acetylation in the Immunogenicity of Bacterial Polysaccharide Vaccines" - Molecules 23(6) (2018) 1340
  

  The incidence of infectious diseases caused by several bacterial pathogens such as Haemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitidis, has been dramatically reduced over the last 25 years through the use of glycoconjugate vaccines. The structures of the bacterial capsular polysaccharide (CPS) antigens, extracted and purified from microbial cultures and obtained with very high purity, show that many of them are decorated by O-acetyl groups. While these groups are often considered important for the structural identity of the polysaccharides, they play a major role in the functional immune response to some vaccines such as meningococcal serogroup A and Salmonella typhi Vi, but do not seem to be important for many others, such as meningococcal serogroups C, W, Y, and type III Group B Streptococcus. This review discusses the O-acetylation status of CPSs and its role in the immunological responses of these antigens.

  O-acetylation, Bacterial polysaccharide, conjugate vaccines, Bacterial Vaccines, carbohydrate antigens

  NCBI PubMed ID: 29865239
  Publication DOI: 10.3390/molecules23061340
  Journal NLM ID: 100964009
  Publisher: Basel, Switzerland: MDPI
  Correspondence: rino.x.rappuoli@gsk.com
  Institutions: External R&D, GSK Vaccines, 53100 Siena, Italy, External R&D, GSK Vaccines, 53100 Siena, Ital
  
   
  
  Streptococcus pneumoniae 22F
  CSDB ID 13048 (all data & tools)
• Article ID: 5473
  Zou W, Li J, Vinogradov E, Cox A "Removal of cell wall polysaccharide in pneumococcal capsular polysaccharides by selective degradation via deamination" - Carbohydrate Polymers 218 (2019) 199-207
  

  Pneumococcal cell wall polysaccharide (C-PS), a contaminant in pneumococcal capsular polysaccharide (Pn-PS) vaccines is degraded by mild deamination of the 4-amino-2-acetamido-2,4,6-tri-deoxy-galactose (AAT) in C-PS, which was carried out by addition of 5% aqueous sodium nitrite to a solution of polysaccharide in 5% aqueous acetic acid. Glycosidic linkage and functional groups such as O-acetates, phosphodiesters, and pyruvates were preserved under the conditions. The small fragments from degraded C-PS were removed by ultrafiltration or dialysis to provide essentially C-PS free Pn-PS. Because of the presence of AAT in its structure the deamination is not suitable for the purification of type 1 Pn-PS. Meanwhile, the mass and NMR spectroscopic analysis on the deamination products suggests that both type 1 Pn-PS and C-PS degraded following a major pathway of 5,4-hydride shift, cleavage of AAT O5-C1 bond, C1 hemiacetal formation, and its hydrolysis to release neighboring GalA- in type 1 Pn-PS and GalNAc(6-O-PCho)- in C-PS

  mechanism, degradation, deamination, cell wall polysaccharide, pneumococcal capsular polysaccharide

  NCBI PubMed ID: 31221321
  Publication DOI: 10.1016/j.carbpol.2019.03.070
  Journal NLM ID: 8307156
  Publisher: Elsevier
  Correspondence: W. Zou
  Institutions: Human Health Therapeutic Research Center, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
  Methods: 13C NMR, 1H NMR, gel filtration, sugar analysis, MS/MS, MS, dialysis, SEC-HPLC, ultrafiltration, mild deamination
  
   
  
  Streptococcus pneumoniae 22F
  CSDB ID 1963 (all data & tools)
• Article ID: 6386
  Gaikwad WK, Dhere RM, Jana SK, Mallya AD, Soni DJ, Gholap M, Ravenscroft N, Kodam KM "Effect of trifluoroacetic acid on the antigenicity of capsular polysaccharides obtained from various Streptococcus pneumoniae serotypes" - Carbohydrate Polymers 320 (2023) 121204
  

  Determining the safety, antigenicity, and immunogenicity by in vitro and in vivo studies is a prerequisite for the development of new vaccines. And this study investigated it for a vaccine made from Streptococcus pneumoniae serotypes 2, 5, 12F, 18C, and 22F. The crude CPS was purified and partially depolymerized by conventional and trifluoroacetic acid methods. 1H NMR analysis confirmed the identity of the depolymerized CPS which gave similar profiles to reference polysaccharides, except for serotype 18C which was de-O-acetylated during TFA treatment. The antigenicity of the depolymerized CPS prepared by either method was comparable to that of the native CPS for serotypes 2, 5, 18C, and 22F based on multiplex bead based competitive inhibition assay. This study demonstrated a relationship between antigenicity and immunogenicity, which offers more suitable candidates for conjugation. It was found that after partial depolymerization process, the CPS with optimal molecular size resulted in higher antigenicity. The immunogenicity of S. pneumoniae serotype 2 conjugates in mice was evaluated by opsonophagocytic assay and a multiplex bead-based assay, wherein on day 42 after immunization, the total and functional IgG titer was found to be increased by 32-fold.

  Streptococcus pneumoniae, immunogenicity, antigenicity, CRM197, pneumococcal conjugate vaccine, trifluoroacetic acid

  NCBI PubMed ID: 37659807
  Publication DOI: 10.1016/j.carbpol.2023.121204
  Journal NLM ID: 8307156
  Publisher: Elsevier
  Correspondence: R.M. Dhere ; K.M. Kodam
  Institutions: Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa, Department of Technology, Savitribai Phule Pune University, Pune 411007, India, Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India, Research and Development Department, Serum Institute of India Pvt. Ltd, Hadapsar, Pune 411028, India
  Methods: 1H NMR, chemical analysis, inhibition studies, partial depolymerization, immunization, conjugation, fermentation, SEC-HPLC, opsonophagocytic assay
  
   
  
  Streptococcus pneumoniae 22F
  CSDB ID 10697 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130693,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_983931,SB_192,SB_7

• Article ID: 339
  Nnalue NA, Khan GN, Mustafa N "Cross-reactivity between six Enterobacteriaceae complete lipopolysaccharide core chemotypes" - Journal of Medical Microbiology 48(5) (1999) 433-441
  

  To gain insight into the value of lipopolysaccharide (LPS) core determinants for cross-protective immunisation the serological relationships between six complete (LPS) core types from Enterobacteriaceae were investigated. Hyperimmune sera were raised in mice by repeated immunisation with heat-killed strains of Salmonella choleraesuis (Ra core type) or Escherichia coli (core types R1, R2, R3, R4 and K12) and characterised for reactivity with complete and incomplete core chemotypes by ELISA and immunoblotting. Three sera (anti-Ra, anti-R2 and anti-R3) reacted strongly with 3-5 different complete core types whereas the other three (anti-R1, anti-R4 and anti-K12) reacted strongly only with their homologous core types in these assays. Two approaches were used to examine further the structural bases for cross-reactivity between these cores. By the first approach the anti-complete-core sera were tested for cross-reactivity with truncated forms of the Salmonella species core (incomplete cores) derived from core-defective mutants. By the second approach, antisera raised against some core-defective mutants were tested for cross-reactivity with complete cores. The results of these investigations revealed that several pair-wise combinations of core types can be used as immunogens to elicit immune responses that recognise all six core types and that the major determinants which mediate cross-reactivity between complete cores are localised in the outer core region.

  Lipopolysaccharide, core, lipopolysaccharide core, chemotype, Chemotypes, cross-reactivity, crossreactivity, Enterobacteriaceae

  NCBI PubMed ID: 10229540
  Journal NLM ID: 0224131
  Publisher: Reading, England: Society for General Microbiology
  Institutions: Department of Medical Microbiology, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
  Methods: SDS-PAGE, ELISA, biological assays, serological methods, immunoblotting
  
   
  
  Salmonella choleraesuis SN57, Salmonella typhimurium TV119
  CSDB ID 7761 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_131186,IEDB_135818,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_983931,SB_192,SB_7

• Article ID: 339
  Nnalue NA, Khan GN, Mustafa N "Cross-reactivity between six Enterobacteriaceae complete lipopolysaccharide core chemotypes" - Journal of Medical Microbiology 48(5) (1999) 433-441
  

  To gain insight into the value of lipopolysaccharide (LPS) core determinants for cross-protective immunisation the serological relationships between six complete (LPS) core types from Enterobacteriaceae were investigated. Hyperimmune sera were raised in mice by repeated immunisation with heat-killed strains of Salmonella choleraesuis (Ra core type) or Escherichia coli (core types R1, R2, R3, R4 and K12) and characterised for reactivity with complete and incomplete core chemotypes by ELISA and immunoblotting. Three sera (anti-Ra, anti-R2 and anti-R3) reacted strongly with 3-5 different complete core types whereas the other three (anti-R1, anti-R4 and anti-K12) reacted strongly only with their homologous core types in these assays. Two approaches were used to examine further the structural bases for cross-reactivity between these cores. By the first approach the anti-complete-core sera were tested for cross-reactivity with truncated forms of the Salmonella species core (incomplete cores) derived from core-defective mutants. By the second approach, antisera raised against some core-defective mutants were tested for cross-reactivity with complete cores. The results of these investigations revealed that several pair-wise combinations of core types can be used as immunogens to elicit immune responses that recognise all six core types and that the major determinants which mediate cross-reactivity between complete cores are localised in the outer core region.

  Lipopolysaccharide, core, lipopolysaccharide core, chemotype, Chemotypes, cross-reactivity, crossreactivity, Enterobacteriaceae

  NCBI PubMed ID: 10229540
  Journal NLM ID: 0224131
  Publisher: Reading, England: Society for General Microbiology
  Institutions: Department of Medical Microbiology, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
  Methods: SDS-PAGE, ELISA, biological assays, serological methods, immunoblotting
  
   
  
  Escherichia coli HF4704
  CSDB ID 31500 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130693,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 339
  Nnalue NA, Khan GN, Mustafa N "Cross-reactivity between six Enterobacteriaceae complete lipopolysaccharide core chemotypes" - Journal of Medical Microbiology 48(5) (1999) 433-441
  

  To gain insight into the value of lipopolysaccharide (LPS) core determinants for cross-protective immunisation the serological relationships between six complete (LPS) core types from Enterobacteriaceae were investigated. Hyperimmune sera were raised in mice by repeated immunisation with heat-killed strains of Salmonella choleraesuis (Ra core type) or Escherichia coli (core types R1, R2, R3, R4 and K12) and characterised for reactivity with complete and incomplete core chemotypes by ELISA and immunoblotting. Three sera (anti-Ra, anti-R2 and anti-R3) reacted strongly with 3-5 different complete core types whereas the other three (anti-R1, anti-R4 and anti-K12) reacted strongly only with their homologous core types in these assays. Two approaches were used to examine further the structural bases for cross-reactivity between these cores. By the first approach the anti-complete-core sera were tested for cross-reactivity with truncated forms of the Salmonella species core (incomplete cores) derived from core-defective mutants. By the second approach, antisera raised against some core-defective mutants were tested for cross-reactivity with complete cores. The results of these investigations revealed that several pair-wise combinations of core types can be used as immunogens to elicit immune responses that recognise all six core types and that the major determinants which mediate cross-reactivity between complete cores are localised in the outer core region.

  Lipopolysaccharide, core, lipopolysaccharide core, chemotype, Chemotypes, cross-reactivity, crossreactivity, Enterobacteriaceae

  NCBI PubMed ID: 10229540
  Journal NLM ID: 0224131
  Publisher: Reading, England: Society for General Microbiology
  Institutions: Department of Medical Microbiology, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
  Methods: SDS-PAGE, ELISA, biological assays, serological methods, immunoblotting
  
   
  
  Escherichia coli EH100
  CSDB ID 31501 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_136906,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 339
  Nnalue NA, Khan GN, Mustafa N "Cross-reactivity between six Enterobacteriaceae complete lipopolysaccharide core chemotypes" - Journal of Medical Microbiology 48(5) (1999) 433-441
  

  To gain insight into the value of lipopolysaccharide (LPS) core determinants for cross-protective immunisation the serological relationships between six complete (LPS) core types from Enterobacteriaceae were investigated. Hyperimmune sera were raised in mice by repeated immunisation with heat-killed strains of Salmonella choleraesuis (Ra core type) or Escherichia coli (core types R1, R2, R3, R4 and K12) and characterised for reactivity with complete and incomplete core chemotypes by ELISA and immunoblotting. Three sera (anti-Ra, anti-R2 and anti-R3) reacted strongly with 3-5 different complete core types whereas the other three (anti-R1, anti-R4 and anti-K12) reacted strongly only with their homologous core types in these assays. Two approaches were used to examine further the structural bases for cross-reactivity between these cores. By the first approach the anti-complete-core sera were tested for cross-reactivity with truncated forms of the Salmonella species core (incomplete cores) derived from core-defective mutants. By the second approach, antisera raised against some core-defective mutants were tested for cross-reactivity with complete cores. The results of these investigations revealed that several pair-wise combinations of core types can be used as immunogens to elicit immune responses that recognise all six core types and that the major determinants which mediate cross-reactivity between complete cores are localised in the outer core region.

  Lipopolysaccharide, core, lipopolysaccharide core, chemotype, Chemotypes, cross-reactivity, crossreactivity, Enterobacteriaceae

  NCBI PubMed ID: 10229540
  Journal NLM ID: 0224131
  Publisher: Reading, England: Society for General Microbiology
  Institutions: Department of Medical Microbiology, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
  Methods: SDS-PAGE, ELISA, biological assays, serological methods, immunoblotting
  
   
  
  Escherichia coli F653
  CSDB ID 31502 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 339
  Nnalue NA, Khan GN, Mustafa N "Cross-reactivity between six Enterobacteriaceae complete lipopolysaccharide core chemotypes" - Journal of Medical Microbiology 48(5) (1999) 433-441
  

  To gain insight into the value of lipopolysaccharide (LPS) core determinants for cross-protective immunisation the serological relationships between six complete (LPS) core types from Enterobacteriaceae were investigated. Hyperimmune sera were raised in mice by repeated immunisation with heat-killed strains of Salmonella choleraesuis (Ra core type) or Escherichia coli (core types R1, R2, R3, R4 and K12) and characterised for reactivity with complete and incomplete core chemotypes by ELISA and immunoblotting. Three sera (anti-Ra, anti-R2 and anti-R3) reacted strongly with 3-5 different complete core types whereas the other three (anti-R1, anti-R4 and anti-K12) reacted strongly only with their homologous core types in these assays. Two approaches were used to examine further the structural bases for cross-reactivity between these cores. By the first approach the anti-complete-core sera were tested for cross-reactivity with truncated forms of the Salmonella species core (incomplete cores) derived from core-defective mutants. By the second approach, antisera raised against some core-defective mutants were tested for cross-reactivity with complete cores. The results of these investigations revealed that several pair-wise combinations of core types can be used as immunogens to elicit immune responses that recognise all six core types and that the major determinants which mediate cross-reactivity between complete cores are localised in the outer core region.

  Lipopolysaccharide, core, lipopolysaccharide core, chemotype, Chemotypes, cross-reactivity, crossreactivity, Enterobacteriaceae

  NCBI PubMed ID: 10229540
  Journal NLM ID: 0224131
  Publisher: Reading, England: Society for General Microbiology
  Institutions: Department of Medical Microbiology, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
  Methods: SDS-PAGE, ELISA, biological assays, serological methods, immunoblotting
  
   
  
  Escherichia coli F2513
  CSDB ID 31503 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_232584,IEDB_983931,SB_192,SB_7

• Article ID: 339
  Nnalue NA, Khan GN, Mustafa N "Cross-reactivity between six Enterobacteriaceae complete lipopolysaccharide core chemotypes" - Journal of Medical Microbiology 48(5) (1999) 433-441
  

  To gain insight into the value of lipopolysaccharide (LPS) core determinants for cross-protective immunisation the serological relationships between six complete (LPS) core types from Enterobacteriaceae were investigated. Hyperimmune sera were raised in mice by repeated immunisation with heat-killed strains of Salmonella choleraesuis (Ra core type) or Escherichia coli (core types R1, R2, R3, R4 and K12) and characterised for reactivity with complete and incomplete core chemotypes by ELISA and immunoblotting. Three sera (anti-Ra, anti-R2 and anti-R3) reacted strongly with 3-5 different complete core types whereas the other three (anti-R1, anti-R4 and anti-K12) reacted strongly only with their homologous core types in these assays. Two approaches were used to examine further the structural bases for cross-reactivity between these cores. By the first approach the anti-complete-core sera were tested for cross-reactivity with truncated forms of the Salmonella species core (incomplete cores) derived from core-defective mutants. By the second approach, antisera raised against some core-defective mutants were tested for cross-reactivity with complete cores. The results of these investigations revealed that several pair-wise combinations of core types can be used as immunogens to elicit immune responses that recognise all six core types and that the major determinants which mediate cross-reactivity between complete cores are localised in the outer core region.

  Lipopolysaccharide, core, lipopolysaccharide core, chemotype, Chemotypes, cross-reactivity, crossreactivity, Enterobacteriaceae

  NCBI PubMed ID: 10229540
  Journal NLM ID: 0224131
  Publisher: Reading, England: Society for General Microbiology
  Institutions: Department of Medical Microbiology, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
  Methods: SDS-PAGE, ELISA, biological assays, serological methods, immunoblotting
  
   
  
  Escherichia coli W3110
  CSDB ID 31504 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit ; n=10-15
Aglycon: Asn of a protein end: AlaNH2-Asn-Ala-Ser-...
Compound class: N-glycan
Contained glycoepitopes: IEDB_130648,IEDB_135813,IEDB_136095,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141501,IEDB_141584,IEDB_141807,IEDB_149155,IEDB_151531,IEDB_152216,IEDB_190606,IEDB_885822

• Article ID: 468
  Schäffer C, Messner P "Surface-layer glycoproteins: an example for the diversity of bacterial glycosylation with promising impacts on nanobiotechnology" - Glycobiology 14(8) (2004) 31R-42R
  

  Bacterial cell surface layers, referred to simply as S-layers, have been described for all major phylogenetic groups of bacteria, which may indicate their pivotal role for a bacterium in its natural habitat. They have the unique ability to assemble into two-dimensional crystalline arrays that completely cover the bacterial cells. Glycosylation represents the most frequent modification of S-layer proteins. S-layer glycoproteins constitute a class of glycoconjugates first isolated in the mid-1970s, but S-layer glycoprotein research is still being regarded as an 'exotic field of glycobiology,' possibly because of its 'noneukaryotic' character. Extensive work over the past 30 years provided evidence of an enormous diversity of S-layer glycoproteins that have been created in nature over 3 billion years of prokaryotic evolution. These glycoconjugates are substantially different from eukaryotic glycoproteins, with regard to both composition and structure; nevertheless, some general structural concepts may be deduced. The awareness of the high application potential of S-layer glycoproteins, especially in combination with their intrinsic cell surface display feature, in the field of modern nanobiotechnology as a base for glycoengineering has recently led to the investigation of the S-layer protein glycosylation process at the molecular level, which has lagged behind the structural studies due to the lack of suitable molecular tools. From that work an even more interesting picture of this class of glycoconjugates is emerging. The availability of purified enzymes from S-layer glycan biosynthesis pathways exhibiting increased stabilities and/or rare sugar specificities in conjunction with preliminary genomic data on S-layer glycan biosynthesis clusters will pave the way for the rational design of S-layer neoglycoproteins.

  LPS, bacterial glycosylation, genomic glycosylation loci, glycan diversity, glycoengineering, S-layer nanoglycobiology

  NCBI PubMed ID: 15044388
  Publication DOI: 10.1093/glycob/cwh064
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Correspondence: paul.messner@boka.ac.at
  Institutions: Center for NanoBiotechnology, University of Applied Life Sciences and Natural Resources, Gregor-Mendel-Strasse 33, A-1180 Wien, Austria
  
   
  
  Halobacterium halobium R1M1
  CSDB ID 31629 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-glycoprotein
Contained glycoepitopes: IEDB_136044,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_153217,IEDB_190606,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88

• Article ID: 468
  Schäffer C, Messner P "Surface-layer glycoproteins: an example for the diversity of bacterial glycosylation with promising impacts on nanobiotechnology" - Glycobiology 14(8) (2004) 31R-42R
  

  Bacterial cell surface layers, referred to simply as S-layers, have been described for all major phylogenetic groups of bacteria, which may indicate their pivotal role for a bacterium in its natural habitat. They have the unique ability to assemble into two-dimensional crystalline arrays that completely cover the bacterial cells. Glycosylation represents the most frequent modification of S-layer proteins. S-layer glycoproteins constitute a class of glycoconjugates first isolated in the mid-1970s, but S-layer glycoprotein research is still being regarded as an 'exotic field of glycobiology,' possibly because of its 'noneukaryotic' character. Extensive work over the past 30 years provided evidence of an enormous diversity of S-layer glycoproteins that have been created in nature over 3 billion years of prokaryotic evolution. These glycoconjugates are substantially different from eukaryotic glycoproteins, with regard to both composition and structure; nevertheless, some general structural concepts may be deduced. The awareness of the high application potential of S-layer glycoproteins, especially in combination with their intrinsic cell surface display feature, in the field of modern nanobiotechnology as a base for glycoengineering has recently led to the investigation of the S-layer protein glycosylation process at the molecular level, which has lagged behind the structural studies due to the lack of suitable molecular tools. From that work an even more interesting picture of this class of glycoconjugates is emerging. The availability of purified enzymes from S-layer glycan biosynthesis pathways exhibiting increased stabilities and/or rare sugar specificities in conjunction with preliminary genomic data on S-layer glycan biosynthesis clusters will pave the way for the rational design of S-layer neoglycoproteins.

  LPS, bacterial glycosylation, genomic glycosylation loci, glycan diversity, glycoengineering, S-layer nanoglycobiology

  NCBI PubMed ID: 15044388
  Publication DOI: 10.1093/glycob/cwh064
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Correspondence: paul.messner@boka.ac.at
  Institutions: Center for NanoBiotechnology, University of Applied Life Sciences and Natural Resources, Gregor-Mendel-Strasse 33, A-1180 Wien, Austria
  
   
  
  Halobacterium halobium R1M1
  CSDB ID 31631 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_149136,IEDB_151531,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983931,SB_192

• Article ID: 1107
  Petersson C, Jachymek W, Kenne L, Niedziela T, Lugowski C "Structural studies of the O-specific chain of Hafnia alvei strain PCM1190 lipopolysaccharide" - Carbohydrate Research 298 (1997) 219-227
  

  The structure of the O-specific side-chain of the lipopolysaccharide of Hafnia alvei strain PCM1190 has been investigated. Methylation analysis, partial acid hydrolysis, Smith degradation, NMR spectroscopy, MALDI-TOF, and FAB mass spectrometry in combination with colision-induced-decomposition MS/MS were the principal methods used. It was concluded that the polysaccharide is composed of heptasaccharide repeating units having the following structure: [see formula in text].

  Lipopolysaccharide, O-antigen, Hafnia alvei, MS/MS

  NCBI PubMed ID: 9183004
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, S-750 07 Uppsala, Sweden, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Czerska 12, PL-53-114 Wroclaw, Poland
  Methods: methylation, NMR-2D, FAB-MS, partial acid hydrolysis, NMR, Smith degradation, MALDI-TOF MS, CID-MS/MS
  
   
  
  Hafnia alvei PCM 1190
  CSDB ID 4049 (all data & tools)
• Article ID: 4329
  Knirel YA "Structure of O-antigens" - Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
  

  The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.

  Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis

  Publication DOI: 10.1007/978-3-7091-0733-1_3
  Publisher: Springer
  Correspondence: knirel@ioc.ac.ru
  Editors: Knirel YA, Valvano MA
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Hafnia alvei 1190
  CSDB ID 27551 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_136095,IEDB_137472,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_153755,IEDB_190606,IEDB_983931,SB_192

• Article ID: 1288
  Yamamoto Y, Nunome T, Yamauchi R, Kato K, Sone Y "Structure of an exocellular polysaccharide of Lactobacillus helveticus TN-4, a spontaneous mutant strain of Lactobacillus helveticus TY1-2" - Carbohydrate Research 275(2) (1995) 319-332
  

  Lactobacillus helveticus strain TN-4, a spontaneous mutant strain of Lactobacillus helveticus TY1-2, produced an exocellular polysaccharide from reconstituted skim milk. On the basis of the results of methylation analysis, enzymatic digestion, mild Smith degradation, mild acid hydrolysis, acetolysis, and 1D and 2D 1H NMR spectroscopy, it was concluded that the polysaccharide has a D-galactofuranose containing hexasaccharide repeating unit with the following structure: [formula see text]

  NMR, structure, strain, polysaccharide, exocellular polysaccharide, mutant, Lactobacillus helveticus, lactic acid, milk, Exocellular polysaccharide; Lactobacillus helveticus TN-4; Lactobacillus helveticus TYI-2, Lactobacillus helveticus TN-4, Lactobacillus helveticus TYI-2

  NCBI PubMed ID: 8529226
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: United Graduate School of Agricultural Science, Gifu University, Gifu 501-11, Japan, Takeda Food Products, Ltd., 3 - 20 Imoji, Itami, Hyougo 664, Japan, Faculty of Human Life Science, Osaka City University, Sugimoto-cho, Sumiyoshi-ku, Osaka 558, Japan
  Methods: methylation, NMR-2D, NMR, mild acid hydrolysis, Smith degradation, acetolysis, b-galactosidase digestion
  
   
  
  Lactobacillus helveticus TN-4
  CSDB ID 6004 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: Escherichia coli K-12 core
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_137472,IEDB_141807,IEDB_151531,IEDB_190606

• Article ID: 1403
  Clarke BR, Bronner D, Keenleyside WJ, Severn WB, Richards JC, Whitfield C "Role of Rfe and RfbF in the initiation of biosynthesis of D-galactan I, the lipopolysaccharide O antigen from Klebsiella pneumoniae serotype O1" - Journal of Bacteriology 177(19) (1995) 5411-5418
  

  The 6.6-kb rfb gene cluster from Klebsiella pneumoniae serotype O1 (rfbKpO1) contains six genes whose products are required for the biosynthesis of a lipopolysaccharide O antigen with the following repeating unit structure: 33-b-D-Galf-133-a-D-Galp-13(D-galactan I). rfbFKpO1 is the last gene in the cluster, and its gene product is required for the initiation of D-galactan I synthesis. Escherichia coli K-12 strains expressing the RfbFKpO1 polypeptide contain dual galactopyranosyl and galactofuranosyl transferase activity. This activity modifies the host lipopolysaccharide core by adding the disaccharide b-D-Galf-133-a-D-Galp, representing a single repeating unit of D-galactan I. The formation of the lipopolysaccharide substituted either with the disaccharide or with authentic polymeric D-galactan I is dependent on the activity of the Rfe enzyme. Rfe (UDP-GlcpNAc::undecaprenylphosphate GlcpNAc-1-phosphate transferase) catalyzes the formation of the lipid-linked biosynthetic intermediate to which galactosyl residues are transferred during the initial steps of D-galactan I synthesis. The rfbFKpO1 gene comprises 1,131 nucleotides, and the predicted polypeptide consists of 373 amino acid residues with a predicted Mr of 42,600. A polypeptide with an Mr of 42,000 was evident in sodium dodecyl sulfate-polyacrylamide gels when rfbKpO1 was expressed behind the T7 promoter. The carboxyterminal region of RfbFKpO1 shares similarity with the carboxy terminus of RfpB, a galactopyranosyl transferase which is involved in the synthesis of the type 1 O antigen of Shigella dysenteriae.

  Lipopolysaccharide, biosynthesis, antigen, LPS, role, serotype, O-antigen, O antigen, Klebsiella, Klebsiella pneumoniae, D-galactan, initiation

  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: cwhitfie@micro.uoguelph.ca
  Institutions: Department of Microbiology, University of Guelph, Guelph, Canada
  Methods: genetic methods, biochemical methods
  
   
  
  Escherichia coli K12 (mutant)
  CSDB ID 6649 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: GPI-anchor
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130701,IEDB_131186,IEDB_134624,IEDB_135818,IEDB_136104,IEDB_136906,IEDB_137472,IEDB_140116,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_141829,IEDB_142346,IEDB_142347,IEDB_142348,IEDB_143632,IEDB_144983,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_153220,IEDB_176772,IEDB_190606,IEDB_474450,IEDB_983930,SB_136,SB_163,SB_191,SB_196,SB_198,SB_44,SB_67,SB_7,SB_72

• Article ID: 1736
  McConville MJ, Ferguson MAJ "The structure, biosynthesis and function of glycosylated phosphatidylinositols in the parasitic protozoa and higher eukaryotes" - Biochemical Journal 294 (1993) 305-324
  

  No abstract available

  NCBI PubMed ID: 8373346
  Publication DOI: 10.1042/bj2940305
  Journal NLM ID: 2984726R
  Publisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
  Institutions: Department of Biochemistry, University of Dundee, U.K., Department of Biochemistry, University of Dundee, U.K
  
   
  
  Trypanosoma brucei
  CSDB ID 106315 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: glycosyldiacylglycerol
Compound class: glycolipid
Contained glycoepitopes: IEDB_137472,IEDB_190606

• Article ID: 1744
  Reeves RE, Latour NG, Lousteau RJ "A glycerol galactofuranoside from the lipid of an anaerobe" - Biochemistry 3 (1964) 1248-1249
  

  The lipid from an anaerobic organism provisionally designated Bacteroides symbiosus was found to contain D-galactose. Alkaline hydrolysis of the lipid yielded a new glycerol galactoside, specific rotation -73°, with a crystalline hexabenzoate, mp 133-134°, specific rotation -6°. The properties of the new galactoside indicate it to be a 1-glycerol β-D-galactofuranoside. This appears to be the first recorded recognition of a naturally occurring galactofuranoside.

  NCBI PubMed ID: 14229667
  Publication DOI: 10.1021/bi00897a011
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Institutions: Department of Biochemistry, Louisiana State University School of Medicine, New Orleans
  
   
  
  Bacteroides symbiosus
  CSDB ID 106870 (all data & tools)
• Article ID: 4173
  Mayberry WR, Smith PF "Structures and properties of acyl diglucosylcholesterol and galactofuranosyl diacylglycerol from Acholeplasma axanthum" - Biochimica et Biophysica Acta 752 (1983) 434-443
  

  Acholeplasma axanthum is one of the few procaryotes, and the only member of the Mollicutes, known to contain phosphosphingolipids. Examination of strain S743 for glycolipids revealed the presence of glucosides of cholesterol and galactosides of glycerol as the predominant glycolipids. The major component is acylated diglucosylcholesterol, followed by monogalactosyldiacylglycerol and monoglucosylcholesterol. The glucose residues of the sterol-based compounds appear to be α-linked pyranoses, while the galactose of the glycerol-based lipid is an α-linked furanose. The "glycolipid' fraction also contained N-(3-hydroxy)acyl sphinganines with varying degrees of O-acylation. None of these ceramide derivatives was linked to carbohydrate. The major glycolipid, tentatively identified as α-D-glucopyranosyl-(1→3)-(O-acyl)-α-D-glucopyranosyl-(1→3)-cholesterol, along with its deacylated derivative, appears to be the first reported instance of steryl diglycosides among procaryotes, in contrast to the steryl monoglycosides, which are common to other mycoplasmata and some spirochetes.

  NCBI PubMed ID: 6871237
  Publication DOI: 10.1016/0005-2760(83)90273-4
  Journal NLM ID: 0217513
  Publisher: Elsevier
  Institutions: Department of Microbiology, East Tennessee State University, Johnson City, TN, U.S.A., Department of Microbiology, University of South Dakota, Vermillion, SD, U.S.A.
  Methods: periodate oxidation, IR, TLC, GLC, enzymatic digestion, solvolysis, chromium trioxide oxidation
  
   
  
  Acholeplasma axanthum S743 ATCC 25176
  CSDB ID 108912 (all data & tools)