Show legend Show as text

Structure type: oligomer
Aglycon: OSE
Trivial name: tetrasaccharide repeating unit
Contained glycoepitopes: IEDB_130701,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144983,IEDB_149549,IEDB_151531,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 1015
  Mukherjee I, Das SK, Mukherjee A, Roy N "Synthesis of the tetrasaccharide related to the repeating unit of the antigen from Shigella dysenteriae type 5" - Carbohydrate Research 325 (2000) 245-252
  

  Starting from L-rhamnose, D-mannose and 2-amino-2-deoxy-D-glucose hydrochloride, two disaccharide blocks, namely, ethyl 2,4-di-O-benzyl-3-O-[(R)-1-(methoxycarbonyl)ethyl]-α-L-rhamnopyranosyl-(1→3)-2-O-acetyl-4,6-di-O-benzyl-1-thio-α-D-mannopyranoside and 2-(trimethylsilyl)ethyl 2-O-acetyl-3,6-di-O-benzyl-α-D-mannopyranosyl-(1→3)-4,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside, were synthesised and then allowed to react in the presence of N-iodosuccinimide and trifluoromethane sulfonic acid to give a tetrasaccharide derivative. This compound was converted into 2-(trimethylsilyl)ethyl 2,4-di-O-benzyl-3-O-[(R)-1-(methoxycarbonyl)ethyl]-α-L-rhamno- pyranosyl-(1→3)-2-O-acetyl-4,6-di-O-benzyl-α-D-mannopyranosyl-(1→4)-2-O-acetyl-3,6-di-O-benzyl-α-D-mannopyranosyl-(1→3)-2-acetamid o-4,6-di-O-benzyl-2-deoxy-β-D-glucopyranoside, which on hydrogenolysis, afforded the methyl ester 2-(trimethylsilyl)ethyl glycoside of the tetrasaccharide related to the repeating unit of the O-antigen from Shigella dysenteriae type 5.

  synthesis, antigen, Shigella, Shigella dysenteriae type 5, tetrasaccharide repeating unit

  NCBI PubMed ID: 10839118
  Publication DOI: 10.1016/s0008-6215(00)00011-2
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: benr@mahendra.iacs.res.in
  Institutions: Department of Biological Chemistry, Indian Association for the Cultivation of Sciences, Calcutta, India
  
   
  
  Shigella dysenteriae 5
  CSDB ID 3710 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115576,IEDB_130701,IEDB_140116,IEDB_144983,IEDB_149549,IEDB_152206,IEDB_164174,IEDB_76933,IEDB_983930,SB_197,SB_44,SB_67,SB_72

• Article ID: 1193
  Senchenkova SN, Shashkov AS, Knirel YA, McGovern JJ, Moran AP "The O-specific polysaccharide chain of Campylobacter fetus serotype A lipopolysaccharide is a partially O-acetylated 1,3-linked a-D-mannan" - European Journal of Biochemistry 245 (1997) 637-641
  

  Lipopolysaccharide, LPS, structure, structural, polysaccharide, serotype, D-mannose, repeating unit, chain, determination, Campylobacter, O-specific, O-specific polysaccharide, linear, monosaccharide, mannan, homopolymer, Campylobacter fetus, O-side chain, D-mannan

  Publication DOI: 10.1111/j.1432-1033.1997.00637.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D.Zelinsky Institute of Organic Chemistry,Russian Academy of Sciences,Moscow,Russia
  Methods: NMR
  
   
  
  Campylobacter fetus A
  CSDB ID 4637 (all data & tools)
• Article ID: 4328
  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
  
   
  
  Campylobacter fetus A
  CSDB ID 27905 (all data & tools)

Show legend Show as text

Structure type: homopolymer ; n=2-7
Contained glycoepitopes: IEDB_130701,IEDB_144983,IEDB_144996,IEDB_149549,IEDB_149550,IEDB_149551,IEDB_152206,IEDB_474450,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 1397
  Cescutti P, Bigio M, Guarnieri V "Determination of the size and degree of acetyl substitution of oligosaccharides from Neisseria meningitidis group A by ionspray mass spectrometry" - Biochemical and Biophysical Research Communications 224(2) (1996) 444-450
  

  The capsular polysaccharide produced by Neisseria meningitidis group A has the following structure: [formula: see text] [formula: see text] This polysaccharide was partially hydrolysed with acetic acid, and the oligomers obtained were separated by fast performance liquid chromatography. Six fractions were collected and characterised by ionspray mass spectrometry in the positive ion mode. This soft ionisation technique established the size of the obtained oligosaccharides and the degree of O-acetyl substitution for each fraction.

  oligosaccharide, Neisseria meningitidis, Neisseria, capsular, polysaccharide, group, degree, determination, phosphate, Oligosaccharides, hydrolysis, spectrometry, mass spectrometry, Glycosyl phosphate, size, acetyl, depolymerization, liquid chromatography, substitution

  NCBI PubMed ID: 8702408
  Journal NLM ID: 0372516
  Publisher: Academic Press
  Correspondence: cescuitti@univ.trieste.it
  Institutions: Paola Cescutti, Dipartimento di Biochimica, Biotisica e Chimica delle Macromolecole, Trieste, Italy
  Methods: ESI-MS, acid hydrolysis, FPLC
  
   
  
  Neisseria meningitidis A
  CSDB ID 6510 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Contained glycoepitopes: IEDB_130701,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144983,IEDB_149549,IEDB_151531,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 1777
  Knirel YA, Kochetkov NK "The structure of lipopolysaccharides of gram-negative bacteria. III. The structure of O-antigens: A review" - Biochemistry (Moscow) 59(12) (1994) 1325-1383
  

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

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

  NCBI PubMed ID: 7533007
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Escherichia coli O58, Shigella dysenteriae 5
  CSDB ID 108653 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Contained glycoepitopes: IEDB_130701,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144983,IEDB_149549,IEDB_151531,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 2355
  Dmitriev BA, Knirel YA, Kochetkov NK, Jann B, Jann K "Cell-wall lipopolysaccharide of the 'Shigella-like' Escherichia coli 058. Structure of the polysaccharide chain." - European Journal of Biochemistry 79(1) (1977) 111-115
  

  Two lipopolysaccharide preparations were obtained from Escherichia coli 058 by extraction with 45% aqueous phenol and fractional precipitation with cetyltrimethyl ammonium bromide (Cetavlon). Chemical analysis and polyacrylamide gel electrophoresis in the presence of sodium dodecylsulfate showed that the two preparations differed only in the extent of the O-specific polysaccharide moiety. The O-specific polysaccharide was characterized with proton magnetic resonance and infrared spectroscopy, optical rotation and paper electrophoresis. Using gas-liquid chromatography and ion-exchange chromatography, it was shown to contain D-mannose, 2-acetamido-2-deoxy-D-glucose, 3-O-(R-1'-carboxyethyl)-L-rhamnose (rhamnolactylic acid), and O-acetyl groups in the molar ratios of 2:1:1:1. The polysaccharide and oligosaccharides obtained from it were subjected to methylation and chromic acid oxidation. The results obtained indicated that the polysaccharide consists of tetrasaccharide repeating units in which the trisaccharide β-GlcNAc(1-4)α-Man-(1-4)(2/3-O-Ac)-Man is substituted at C-3 of the non-acetylated mannose with rhamnolactylic acid. The repeating units are joined through α-mannosyl-1-3-glucosamine bonds. This structure is identical with that of the cell wall polysaccharide of Shigella dysenteriae type 5.

  NCBI PubMed ID: 334542
  Publication DOI: 10.1111/j.1432-1033.1977.tb11789.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the U.S.S.R., Moscow, Max-Planck-Institut fur Immunbiologie, Freiburg
  Methods: 1H NMR, methylation, IR, acid hydrolysis, Smith degradation, paper chromatography, paper electrophoresis, gel permeation chromatography
  
   
  
  Escherichia coli O58
  CSDB ID 122454 (all data & tools)
• Article ID: 2970
  Dmitriev BA, Backinowsky LV, Knirel YA, Kochetkov NK "Somatic antigens of Shigella. The structure of the specific polysaccharide chain of Shigella dysenteriae type 5 lipopolysaccharide" - European Journal of Biochemistry 78(2) (1977) 381-387
  

  The specific polysaccharide was released from Shigella dysenteriae type 5 lipopolysaccharide by mild acidic hydrolysis and then purified by gel chromatography on Sephadex G-50. The polysaccharide was built up of residues of D-mannose, 2-acetamido-2-deoxy-D-glucose, 3-0-(D-1-carboxyethyl)-L-rhamnose (rhamnolactylic acid) and 0-acetyl groups in a ratio 2:1:1:1. On the basis of radiospectroscopy, methylation analysis, Smith degradation, and chromium trioxide oxidation, the repeating oligosaccharide unit of the polysaccharide can be assigned the following structure: (formula: see text) where GlcNAc is 2-acetamido-2-deoxy-D-glucopyranose, Manp is mannopyranose, RhaLcA is rhammolacytic acid and Ac is an acetyl group. The serological properties of Sh. dysenteriae somatic antigens are discussed in relation to the chemical structures of their specific polysaccharides.

  NCBI PubMed ID: 334537
  Publication DOI: 10.1111/j.1432-1033.1977.tb11750.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia, Institute of Epidemiology and Microbiology, Health Ministry of the Russian Soviet Federal Republic, Moscow
  Methods: 1H NMR, methylation, IR, GC-MS, GLC, paper chromatography, composition analysis, gel chromatography, optical rotation measurent
  
   
  
  Shigella dysenteriae 5
  CSDB ID 122453 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen, polysaccharide
Contained glycoepitopes: IEDB_130701,IEDB_136044,IEDB_137472,IEDB_1394181,IEDB_141794,IEDB_144983,IEDB_149549,IEDB_152206,IEDB_190606,IEDB_983930,SB_165,SB_166,SB_187,SB_195,SB_44,SB_67,SB_7,SB_72,SB_88

• Article ID: 3169
  Karapetyan G, Kaczyński Z, Iacobellis NS, Evidente A, Holst O "The structure of the O-specific polysaccharide of the lipopolysaccharide from Burkholderia gladioli pv. agaricicola" - Carbohydrate Research 341(7) (2006) 930-934
  

  A neutral O-specific polysaccharide containing d-mannose, d-rhamnose and d-galactose was obtained by mild acid hydrolysis of the lipopolysaccharide of the plant pathogenic bacterium Burkholderia gladioli pv. agaricicola. By means of compositional analyses and NMR spectroscopy, the chemical repeating unit of the polymer was identified as a linear trisaccharide of the structure shown below, in which the mannose residue was quantitatively acetylated at C2.

  Lipopolysaccharide, NMR spectroscopy, O-specific polysaccharide, mushroom disease, Agaricus bitorquis, Burkholderia gladioli pv. agaricicola

  NCBI PubMed ID: 16516174
  Publication DOI: 10.1016/j.carres.2006.02.010
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: Otto Holst
  Institutions: Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, D-23845 Borstel, Germany, Dipartimento di Biologia, Difesa e Biotecnologie Agro Forestali, Università degli Studi della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, composition analysis, NMR-1D
  
   
  
  Burkholderia gladioli pv. agaricicola ICMP 11096
  CSDB ID 20158 (all data & tools)
• Article ID: 4328
  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
  
   
  
  Burkholderia gladioli pv. agaricicola
  CSDB ID 27888 (all data & tools)
• Article ID: 5143
  Cloutier M, Muru K, Ravicoularamin G, Gauthier C "Polysaccharides from Burkholderia species as targets for vaccine development, immunomodulation and chemical synthesis" - Natural Product Reports 35(12) (2018) 1251-1293
  

  Burkholderia species are a vast group of human pathogenic, phytopathogenic, and plant- or environment-associated bacteria. B. pseudomallei, B. mallei, and B. cepacia complex are the causative agents of melioidosis, glanders, and cystic fibrosis-related infections, respectively, which are fatal diseases in humans and animals. Due to their high resistance to antibiotics, high mortality rates, and increased infectivity via the respiratory tract, B. pseudomallei and B. mallei have been listed as potential bioterrorism agents by the Centers for Disease Control and Prevention. Burkholderia species are able to produce a large network of surface-exposed polysaccharides, i.e., lipopolysaccharides, capsular polysaccharides, and exopolysaccharides, which are virulence factors, immunomodulators, major biofilm components, and protective antigens, and have crucial implications in the pathogenicity of Burkholderia-associated diseases. This review provides a comprehensive and up-to-date account regarding the structural elucidation and biological activities of surface polysaccharides produced by Burkholderia species. The chemical synthesis of oligosaccharides mimicking Burkholderia polysaccharides is described in detail. Emphasis is placed on the recent research efforts toward the development of glycoconjugate vaccines against melioidosis and glanders based on synthetic or native Burkholderia oligo/polysaccharides.

  lipopolysaccharides, Burkholderia, capsular polysaccharides, Oligosaccharides, glycoconjugate vaccines, antigens, exopolysaccharides, surface polysaccharide, virulence factor, Biofilm, chemical synthesis, bioterrorism

  Publication DOI: 10.1039/C8NP00046H
  Journal NLM ID: 8502408
  Publisher: London: Royal Society of Chemistry
  Correspondence: charles.gauthier@iaf.inrs.ca
  Institutions: INRS-Institut Armand-Frappier, Universite du Quebec, 531, boul. des Prairies, Laval, Canada
  
   
  
  Burkholderia gladioli pv. agaricicola ICMP 11096
  CSDB ID 12529 (all data & tools)
• Article ID: 5623
  Andolfi A, Cimmino A, Cantore PL, Iacobellis NS, Evidente A "Bioactive and structural metabolites of pseudomonas and burkholderia species causal agents of cultivated mushrooms diseases" - Perspectives in Medicinal Chemistry 2 (2008) 81-112
  

  Pseudomonas tolaasii, P. reactans and Burkholderia gladioli pv. agaricicola, are responsible of diseases on some species of cultivated mushrooms. The main bioactive metabolites produced by both Pseudomonas strains are the lipodepsipeptides (LDPs) tolaasin I and II and the so called White Line Inducing Principle (WLIP), respectively, LDPs which have been extensively studied for their role in the disease process and for their biological properties. In particular, their antimicrobial activity and the alteration of biological and model membranes (red blood cell and liposomes) was established. In the case of tolaasin I interaction with membranes was also related to the tridimensional structure in solution as determined by NMR combined with molecular dynamic calculation techniques. Recently, five news minor tolaasins, tolaasins A-E, were isolated from the culture filtrates of P. tolaasii and their chemical structure was determined by extensive use of NMR and MS spectroscopy. Furthermore, their antimicrobial activity was evaluated on target micro-organisms (fungi-including the cultivated mushrooms Agaricus bisporus, Lentinus edodes, and Pleurotus spp.-chromista, yeast and bacteria). The Gram positive bacteria resulted the most sensible and a significant structure-activity relationships was apparent. The isolation and structure determination of bioactive metabolites produced by B. gladioli pv. agaricicola are still in progress but preliminary results indicate their peptide nature. Furthermore, the exopolysaccharide (EPS) from the culture filtrates of B. gladioli pv. agaricicola, as well as the O-chain and lipid A, from the lipopolysaccharide (LPS) of the three bacteria, were isolated and the structures determined

  lipopolysaccharides, exopolysaccharides, Pseudomonas tolaasii, bacterial diseases, cultivated mushrooms, Pseudomonas reactans, Burkholderia gladioli pv. agaricicola, antimicrobial activity, lipodepsipetides, mycopathogenic bacteria, permeabilising effects on membranes

  NCBI PubMed ID: 19787100
  Journal NLM ID: 101322827
  Publisher: Thousand Oaks, CA: SAGE Publications
  Correspondence: evidente@unina.it
  Institutions: Dipartimento di Scienze del Suolo, della Pianta, dell’Ambiente e delle Produzioni Animali, Università di Napoli Federico II, Portici, Italy, Dipartimento di Biologia, Difesa e Biotecnologie Agro-Forestali, Università degli Studi della Basilicata, Potenza, Italy
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, GC-MS, 31P NMR, acid hydrolysis, extraction, acetylation, MALDI-TOF
  
   
  
  Burkholderia gladioli pv. agaricicola ICMP 1096
  CSDB ID 47809 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_130701,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144983,IEDB_149549,IEDB_151531,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 3196
  Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" - FEMS Microbiology Reviews 30(3) (2006) 382-403
  

  Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/

  NMR, structure, serotype, O-antigen, Enterobacteriacea, database

  NCBI PubMed ID: 16594963
  Publication DOI: 10.1111/j.1574-6976.2006.00016.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: andrej.weintraub@ki.se
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  
   
  
  Escherichia coli O58
  CSDB ID 20660 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130422,IEDB_130701,IEDB_136105,IEDB_144983,IEDB_149549,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 3466
  Fernandez de Cordoba FJ, Rodríguez-Carvajal MA, Tejero-Mateo P, Corzo J, Gil-Serrano AM "Structure of the O-Antigen of the Main Lipopolysaccharide Isolated from Sinorhizobium fredii SMH12" - Biomacromolecules 9(2) (2008) 678-685
  

  The lipopolysaccharide of Sinorhizobium fredii SMH12, a wide-range host bacterium isolated from nodulated soybean plants growing in Vietnam, has been studied. Isolation of lipopolysaccharide by the phenol-water method leads to a mixture of two polysaccharides; polyacrylamide gel electrophoresis indicates that both are possibly lipopolysaccharides. The structures of the O-antigen of the main lipopolysaccharide and its deacetylated form are determined by sugar and methylation analysis, partial hydrolysis, lithium degradation, ESI-MS/MS, and NMR studies. Here we show that the fast-growing S. fredii SMH12 produces a lipopolysaccharide whose O-antigen has a repeating unit consisting of the trisaccharide →4)-α-D-GalpA-(1→3)-2-O-Ac-α-L-Rhap-(1→3)-2-O-Ac-α-D-Manp-(1→. The position O-6 of the mannose residue in the repeating unit is unsubstituted, acetylated, or methylated in an approximate ratio 1:1:2. The tandem mass spectrometry studies rule out both an alternating and a random distribution of methyl groups and suggest the existence of zones in the polysaccharide rich in methyl groups interspersed with zones without methyl groups

  Lipopolysaccharide, NMR, O-antigen, Sinorhizobium

  NCBI PubMed ID: 18208318
  Publication DOI: 10.1021/bm701011d
  Journal NLM ID: 100892849
  Publisher: Washington, DC: American Chemical Society
  Correspondence: agil@us.es
  Institutions: Department of Organic Chemistry, Faculty of Chemistry, University of Seville, 41071 Sevilla, Spain, Department of Biochemistry and Molecular Biology, Faculty of Biology, University of La Laguna,E-38206 La Laguna, Spain
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, partial acid hydrolysis, ESI-MS, composition analysis, CID-MS/MS, PAGE
  
   
  
  Sinorhizobium fredii SMH12
  CSDB ID 31138 (all data & tools)

Show legend Show as text

Structure type: monomer
Trivial name: 2-acetamido-2-deoxy-α-D-mannose
Contained glycoepitopes: IEDB_130701,IEDB_144983,IEDB_149549,IEDB_152206,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 3474
  Glaze PA, Watson DC, Young NM, Tanner ME "Biosynthesis of CMP-N,N'-diacetyllegionaminic acid from UDP-N,N'-diacetylbacillosamine in Legionella pneumophila" - Biochemistry 47(10) (2008) 3272-3282
  

  Legionaminic acid is a nine-carbon α-keto acid that is similar in structure to other members of the sialic acid family that includes neuraminic acid and pseudaminic acid. It is found as a component of the lipopolysaccharide in several bacterial species and is perhaps best known for its presence in the O-antigen of the causative agent of Legionnaires' disease, Legionella pneumophila. In this work, the enzymes responsible for the biosynthesis and activation of N, N'-diacetyllegionaminic acid are identified for the first time. A cluster of three L. pneumophila genes bearing homology to known sialic acid biosynthetic genes (neuA,B,C) were cloned and overexpressed in Escherichia coli. The NeuC homologue was found to be a hydrolyzing UDP- N, N'-diacetylbacillosamine 2-epimerase that converts UDP- N, N'-diacetylbacillosamine into 2,4-diacetamido-2,4,6-trideoxymannose and UDP. Stereochemical and isotopic labeling studies showed that the enzyme utilizes a mechanism involving an initial anti elimination of UDP to form a glycal intermediate and a subsequent syn addition of water to generate product. This is similar to the hydrolyzing UDP- N-acetylglucosamine 2-epimerase (NeuC) of sialic acid biosynthesis, but the L. pneumophila enzyme would not accept UDP-GlcNAc as an alternate substrate. The NeuB homologue was found to be a N, N'-diacetyllegionaminic acid synthase that condenses 2,4-diacetamido-2,4,6-trideoxymannose with phosphoenolpyruvate (PEP), although the in vitro activity of the recombinant enzyme (isolated as a MalE fusion protein) was very low. The synthase activity was dependent on the presence of a divalent metal ion, and the reaction proceeded via a C-O bond cleavage process, similar to the reactions catalyzed by the sialic acid and pseudaminic acid synthases. Finally, the NeuA homologue was shown to possess the CMP- N, N'-diacetyllegionaminic acid synthetase activity that generates the activated form of legionaminic acid used in lipopolysaccharide biosynthesis. Together, the three enzymes constitute a pathway that converts a UDP-linked bacillosamine derivative into a CMP-linked legionaminic acid derivative

  O-antigen, lipopolysaccharide biosynthesis, pseudaminic acid, neuraminic acid, Legionella pneumophila, legionaminic acid, Legionella, bacillosamine

  NCBI PubMed ID: 18275154
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Correspondence: mtanner@chem.ubc.ca
  Institutions: Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
  Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, 31P NMR, genetic methods, biochemical methods
  
   
  
  Legionella pneumophila
  CSDB ID 22961 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130701,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144983,IEDB_149549,IEDB_151531,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 3530
  Perepelov AV, Senchenkova SN, Shashkov AS, Knirel YA, Liu B, Feng L, Wang L "Antigenic polysaccharides of bacteria. 41. Structures of the O-specific polysaccharides of Shigella dysenteriae types 4 and 5 revised by NMR spectroscopy" - Russian Journal of Bioorganic Chemistry 34(4) (2008) 460-467
  

  The earlier established structures of the acidic O-specific polysaccharides from two typical strains of the Shigella dysenteriae bacterium were revised using modern NMR spectroscopy techniques. In particular, the configurations of the glycosidic linkages of GlcNAc (S. dysenteriae type 4) and mannose (S. dysenteriae type 5) residues were corrected. In addition, the location of the sites of non-stoichiometric O-acetylation in S. dysenteriae type 4 was determined: the lateral fucose residue was shown to be occasionally O-acetylated; also, theposition of the O-acetyl group present at the stoichiometric quantity in S. dysenteriae type 5 was corrected. The revised structures of the polysaccharides studied are shown below. The known identity of theO-specific polysaccharide structures of S. dysenteriae type 5 and Escherichia coli O58 was confirmed by 13C NMR spectroscopy and, hence, the structure of the E. coli O58 polysaccharide should be revised in the same manner.

  structure, O-antigen, NMR spectroscopy, O-specific polysaccharide, O-Specific polysaccharide structure, Shigella dysenteriae

  NCBI PubMed ID: 18695724
  Publication DOI: 10.1134/S1068162008040109
  Journal NLM ID: 9420101
  Publisher: Springer Science and Business Media
  Correspondence: perepel@ioc.ac.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia,TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, China
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, sugar analysis, GLC, mild acid hydrolysis, alkaline degradation, Smith degradation, NMR-1D
  
   
  
  Shigella dysenteriae 5, Escherichia coli O58
  CSDB ID 23216 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130422,IEDB_130701,IEDB_136105,IEDB_144983,IEDB_149549,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 3592
  Fernandez de Cordoba FJ, Rodríguez-Carvajal MA, Cacada FJ, Tejero-Mateo P, Gil-Serrano AM, Jiménez-Barbero J "Solution Conformation and Dynamics of the O-Antigen of the Major Lipopolysaccharide from Sinorhizobium fredii SMH12" - European Journal of Organic Chemistry (20) (2008) 3469-3473
  

  The conformational and dynamic behavior of the O-antigen of the lipopolysaccharide of Sinorhizobium fredii SMH12, a wide-range host bacterium isolated from nodulated soybean plants growing in Vietnam, was studied. The O-antigenhas a repeating unit consisting of the trisaccharide 4)--D-GalpA-(13)-2-O-Ac--L-Rhap-(13)-2-O-Ac--D-Manp-(1, where the O-6 position of the mannose residue in the repeating unit is unsubstituted, acetylated, or methylated in an approximate ratio 1:1:2. For the analysis of the conformational and dynamic behavior, the deacetylated polysaccharide was employed. A combination of NMR spectroscopic methods assisted by molecular mechanics and dynamic simulations was employed to deduce its major conformational and dynamic features.

  lipopolysaccharides, antigens, molecular dynamics, NMR spectroscopy, conformation analysis, Sinorhizobium fredii

  Publication DOI: 10.1002/ejoc.200800190
  Journal NLM ID: 9805750
  Publisher: Wiley-VCH
  Correspondence: rcarvaj@us.es
  Institutions: Department of Organic Chemistry, Faculty of Chemistry, University of Seville, 41012 Sevilla, Spain, Department of Protein Science, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
  Methods: 13C NMR, 1H NMR, NMR-2D, NMR-1D, CID-MS/MS
  
   
  
  Sinorhizobium fredii SMH12
  CSDB ID 23421 (all data & tools)
• Article ID: 3593
  Fernandez de Cordoba FJ, Rodríguez-Carvajal MA, Tejero-Mateo P, Gil-Serrano AM "Structure and Conformational Studies of the Disaccharides Derived from the Inner Core of the Lipopolysaccharide Isolated from Sinorhizobium fredii SMH12" - European Journal of Organic Chemistry (34) (2008) 5815-5822
  

  The structure and conformational behaviour of the core region of the lipopolysaccharide isolated from Sinorhizobium fredii SMH12, a wide-ranging host bacterium isolated from nodulated soybean plants growing in Vietnam, have been studied. A mixture of oligosaccharides was isolated from the lipopolysaccharide by mild hydrolysis followed by size-exclusion chromatography. The structures were determined by sugar analysis, ESI-MS/MS and NMR studies. Conformational analysis was performed by molecular dynamics calculations and compared with the NMR spectroscopic data. The results indicate that the core oligosaccharide contains a disaccharide made up of -D-glucopyranuronic acid (14)-linked to D-Kdo. In solution, this disaccharide exists as an equilibrium of three different structures.

  Lipopolysaccharide, conformation, structure, core, chemistry, O-antigen, O antigen, Oligosaccharides, conformational, dynamics, Rhizobium, structure elucidation, conformation analysis, inner core, disaccharide, Sinorhizobium, PDF, disaccharides, organic, Sinorhizobium fredii

  Publication DOI: 10.1002/ejoc.200800613
  Journal NLM ID: 9805750
  WWW link: http://www3.interscience.wiley.com/cgi-bin/fulltext/121470458/PDFSTART
  Publisher: Wiley-VCH
  Correspondence: rcarvaj@us.es
  Institutions: Department of Organic Chemistry, Faculty of Chemistry, University of Seville, 41012 Sevilla, Spain, Department of Protein Science, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
  Methods: 13C NMR, 1H NMR, NMR-2D, GLC-MS, partial acid hydrolysis, sugar analysis, ESI-MS, NMR-1D, CAD-MS/MS
  
   
  
  Sinorhizobium fredii SMH12
  CSDB ID 23422 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130422,IEDB_130701,IEDB_136105,IEDB_144983,IEDB_149549,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 3829
  Carlson RW, Forsberg LS, Kannenberg EL "Lipopolysaccharides in Rhizobium-Legume Symbioses" - Book: Endotoxins: Structure, Function and Recognition (series: Subcellular Biochemistry, 2010, Part 1) (2010) Vol. 53, Chapter 16, 339-386
  

  The establishment of nitrogen-fixing symbiosis between a legume plant and its rhizobial symbiont requires that the bacterium adapt to changing conditions that occur with the host plant that both promotes and allows infection of the host root nodule cell, regulates and resists the host defense response, permits the exchange of metabolites, and contributes to the overall health of the host. This adaptive process involves changes to the bacterial cell surface and, therefore, structural modifications to the lipopolysaccharide (LPS). In this chapter, we describe the structures of the LPSs from symbiont members of the Rhizobiales, the genetics and mechanism of their biosynthesis, the modifications that occur during symbiosis, and their possible functions.

  biosynthesis, lipopolysaccharides, structure, Rhizobium, symbiosis, plant defense

  NCBI PubMed ID: 20593275
  Publication DOI: 10.1007/978-90-481-9078-2_16
  Publisher: Springer Science+Business Media B.V.
  Correspondence: rcarlson@ccrc.uga.edu
  Editors: Wang X, Quinn PJ
  Institutions: Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
  
   
  
  Sinorhizobium fredii SMH12
  CSDB ID 25573 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Trivial name: cepacian
Compound class: EPS
Contained glycoepitopes: IEDB_115136,IEDB_130701,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_1394181,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_146664,IEDB_149549,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_983930,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_36,SB_44,SB_61,SB_67,SB_7,SB_72,SB_88,SB_9

• Article ID: 3999
  Cescutti P, Impallomeni G, Garozzo D, Rizzo R "O-Acetyl location on Cepacian, the principal exopolysaccharide of Burkholderia cepacia complex bacteria" - Carbohydrate Research 346(18) (2011) 2905-2912
  

  Cepacian is an exopolysaccharide produced by the majority of the isolates belonging to the Burkholderia cepacia complex bacteria, a group of 17 species, some of which infect cystic fibrosis patients, sometime with fatal outcome. The repeating unit of cepacian consists of a backbone having a trisaccharidic repeating unit with three side chains, as reported in the formula below. The exopolysaccharide is also acetylated, carrying from one to three acetyl esters per repeating unit, depending on the strain examined. The consequences of O-acetyl substitution in a polysaccharide are important both for its biological functions and for industrial applications, including the preparation of conjugated vaccines, since O-acetyl groups are important immunogenic determinants. The location of acetyl groups was achieved by NMR spectroscopy and ESI mass spectrometry and revealed that these substituents are scattered in non-stoichiometric ratio on many sugar residues in different positions, a feature which adds to the already unique carbohydrate structure of the polysaccharide.

  NMR, polysaccharide structure, ESI-MS, cystic fibrosis, O-Acetyl groups, Burkholderia cepacia complex

  NCBI PubMed ID: 22055818
  Publication DOI: 10.1016/j.carres.2011.10.011
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pcescutti@units.it
  Institutions: Dipartimento di Scienze della Vita, Università di Trieste, via L. Giorgieri 1, 34134 Trieste, Italy, Istituto di Chimica e Tecnologia dei Polimeri, Via Paolo Gaifami 18, 95126 Catania, Italy
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, enzymatic hydrolysis, ESI-MS, de-O-acetylation
  
   
  
  Burkholderia pyrrocinia BTS7
  CSDB ID 26582 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_130701,IEDB_136045,IEDB_137473,IEDB_1391961,IEDB_141501,IEDB_141584,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_146664,IEDB_149549,IEDB_152206,IEDB_152214,IEDB_174333,IEDB_885822,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_72,SB_86

• Article ID: 4065
  Li Y, Perepelov AV, Guo D, Shevelev SD, Senchenkova SN, Shashkov AS, Liu B, Wang L, Knirel YA "Structural and genetic relationships of two pairs of closely related O-antigens of Escherichia coli and Salmonella enterica: E. coli O11/S. enterica O16 and E. coli O21/S. enterica O38" - FEMS Immunology and Medical Microbiology 61(3) (2011) 258-268
  

  O-antigen is a part of the lipopolysaccharide present in the outer membrane of Gram-negative bacteria, which is essential for the full function of the microorganisms and is related to bacterial virulence. Salmonella enterica and Escherichia coli are taxonomically closely related species. In this study, the O-antigen structures of S. enterica O16, O38 and E. coli O11 were determined. It was found that S. enterica O38 and E. coli O21 share the O-antigen structure, whereas those of S. enterica O16 and E. coli O11 are closely related differing only in the presence of a lateral glucose residue and O-acetylation of a mannose residue in the former. The O-antigen gene clusters of S. enterica O16, O38 and E. coli O11 were sequenced and analyzed together with that of E. coli O21 retrieved from Genbank. For each S. enterica/E. coli pair, they were found to contain the same set of genes organized in the same manner and sharing 56% to 78% overall DNA identity. These data suggest that the O-antigen gene clusters of each pair studied originated from a common ancestor, as reported for a number of other known E. coli/S. enterica pairs having identical or closely related O-antigen structures. It has become thus evident that in past the degree of relatedness between the O-antigens of S. enterica and E. coli was underestimated.

  Escherichia coli, Salmonella enterica, O-antigen gene cluster, Glycomics, O-antigen diversity

  NCBI PubMed ID: 21205000
  Publication DOI: 10.1111/j.1574-695X.2010.00771.x
  Journal NLM ID: 9315554
  Publisher: Elsevier
  Correspondence: liubin1981@nankai.edu.cn
  Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, PCR, DNA sequencing, GLC-MS, sugar analysis, acid hydrolysis, Smith degradation, de-O-acetylation, NMR-1D
  
   
  
  Salmonella enterica O16 G1459
  CSDB ID 26889 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130422,IEDB_130701,IEDB_136105,IEDB_144983,IEDB_149549,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 4328
  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
  
   
  
  Sinorhizobium fredii
  CSDB ID 27847 (all data & tools)