Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_131187,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_7,SB_72

• Article ID: 89
  Galbraith L, Wilkinson SG "Structural studies on the O-specific side-chain of lipopolysaccharide from Burkholderia gladioli pv. gladioli strain NCPPB 1891" - Carbohydrate Research 303 (1997) 245-249
  

  A polymeric fraction (the O-antigenic side-chain) has been isolated from the lipopolysaccharide of Burkholderia gladioli pv. gladioli strain NCPPB 1891 after mild acid hydrolysis. The components of the polymer and their molar proportions were L-Rha (1), D-Gal (1), D-Man (1), and O-acetyl (1). By means of chemical degradations and NMR studies, the repeating unit of the polymer was shown to be a linear trisaccharide of the structure shown. [formula: see text]

  Lipopolysaccharide, O-antigen, Burkholderia gladioli

  NCBI PubMed ID: 9352638
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: S.G.Wilkison@chem.hull.ac.uk
  Institutions: School of Chemistry, University of Hull, UK
  Methods: NMR-2D, methylation, NMR, sugar analysis
  
   
  
  Burkholderia gladioli pv. gladioli NCPPB1891
  CSDB ID 2090 (all data & tools)
• Article ID: 1452
  Corsaro MM, De Castro C, Molinaro A, Parrilli M "Structure of lipopolysaccharides from phytopathogenic Gram-negative bacteria" - Book: Recent Research Developments in Phytochemistry (2001) Vol. 5, 119-138
  

  This review collects the structural data of lipopolysaccharide components arising from all phytopathogenic bacteria so far investigated. The structural approaches and the main biological role of these macromolecules are also reported.

  Lipopolysaccharide, lipopolysaccharides, structure, core, lipid A, O-polysaccharide, gram negative bacteria

  WWW link: https://books.google.ru/books/about/Recent_Research_Developments_in_Phytoche.html?id=5CJacgAACAAJ&redir_esc=y
  Publisher: Research Signpost, Trivandrum, India
  Editors: Pandalai SG
  Institutions: Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte S.Angelo Via Cintia, 4, 80126 Napoli, Italy
  
   
  
  Burkholderia gladioli pv. gladioli NCPPB 1891
  CSDB ID 31708 (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. gladioli
  CSDB ID 27887 (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. gladioli NCPPB 1891
  CSDB ID 12530 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131187,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_7,SB_72

• Article ID: 89
  Galbraith L, Wilkinson SG "Structural studies on the O-specific side-chain of lipopolysaccharide from Burkholderia gladioli pv. gladioli strain NCPPB 1891" - Carbohydrate Research 303 (1997) 245-249
  

  A polymeric fraction (the O-antigenic side-chain) has been isolated from the lipopolysaccharide of Burkholderia gladioli pv. gladioli strain NCPPB 1891 after mild acid hydrolysis. The components of the polymer and their molar proportions were L-Rha (1), D-Gal (1), D-Man (1), and O-acetyl (1). By means of chemical degradations and NMR studies, the repeating unit of the polymer was shown to be a linear trisaccharide of the structure shown. [formula: see text]

  Lipopolysaccharide, O-antigen, Burkholderia gladioli

  NCBI PubMed ID: 9352638
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: S.G.Wilkison@chem.hull.ac.uk
  Institutions: School of Chemistry, University of Hull, UK
  Methods: NMR-2D, methylation, NMR, sugar analysis
  
   
  
  Burkholderia gladioli pv. gladioli NCPPB1891
  CSDB ID 2194 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_131187,IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_137485,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144983,IEDB_146664,IEDB_151527,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_190606,IEDB_423153,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_7,SB_72

• Article ID: 713
  Kalelkar S, Glushka J, van Halbeek H, Morris LC, Cherniak R "Structure of the capsular polysaccharide of Clostridium perfringens Hobbs 5 as determiend by NMR spectroscopy" - Carbohydrate Research 299(3) (1997) 119-128
  

  The complete primary structure of the capsular polysaccharide of Clostridium perfringens Hobbs 5, an anaerobic bacterium implicated in food poisoning, was determined. The polysaccharide was isolated from C. perfringens Hobbs 5 cells, after deproteination, by ethanol precipitation and by ion-exchange chromatography. The polysaccharide was comprised of glucose, galactose, mannose, N-acetylglucosamine, N-acetylgalactosamine, and glucuronic acid, in equimolar ratios. Sequence and linkage assignments of the glycosyl residues were obtained by NMR spectroscopy, specifically by the combination of two-dimensional homonuclear TOCSY and NOESY experiments and heteronuclear (1H, 13C) multiple-quantum coherence (HMQC, HMQC-COSY, HMQC-TOCSY and HMBC) experiments. Thus, the envelope polysaccharide of C. perfringens Hobbs 5 was found to be a polymer composed of a hexasaccharide repeating unit with the following structure: [formula: see text] This structure is novel among bacterial cell-surface polysaccharides, and it is the first of many serotypically distinct capsular polysaccharides of C. perfringens to be described.

  NMR, antigen, structure, capsular, polysaccharide, capsular polysaccharide, NMR spectroscopy, spectroscopy, 2D NMR spectroscopy, HMQC, Clostridium, Clostridium perfingens, TOCSY, NOESY

  NCBI PubMed ID: 9163894
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: cherniak@gsu.edu
  Institutions: Department of Chemistry (LBCS), Georgia State University, Atlanta, GA, USA
  Methods: NMR
  
   
  
  Clostridium perfringens Hobbs 5
  CSDB ID 833 (all data & tools)
• Article ID: 5791
  Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" - Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
  

  Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.

  polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component

  Publication DOI: 10.1016/B978-0-12-819475-1.00005-5
  Publisher: Elsevier
  Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
  Editors: Barchi J, Kamerling H
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
  
   
  
  Clostridium perfringens Hobbs 5
  CSDB ID 25099 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_130701,IEDB_131187,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 1679
  Avila JL, Rojas M, Rodas A, Convit J "Parasitic oligosaccharide residues recognized by patients with mucocutaneous and localized cutaneous leishmaniasis" - American Journal of Tropical Medicine and Hygiene 47 (1992) 284-290
  

  Humoral immune responses were studied in 118 Venezuelan patients with either active mucocutaneous (MCL) or localized cutaneous leishmaniasis (LCL). Most patients had elevated antibody levels to the six promastigote oligosaccharide residues studied: galactosyl(α 1-2)galactose, galactosyl(α 1-3)galactose, galactosyl(α 1-6)galactose, galactosyl(α 1-3)mannose, galactofuranosyl(β1-3)mannose, and galactocerebroside. Significantly higher antibody levels were found in patients with MCL against galactosyl(α 1-3)galactose and Leishmania tropica glycoinositol phospholipid (GIPL)-1, GIPL-2, and GIPL-3 compared with patients with LCL. For both clinical forms of American cutaneous leishmaniasis (ACL), the most reactive antigen was galactosyl(α 1-3)galactose, with elevated levels found in 63% and 79% of MCL and LCL patients, respectively. In patients with MCL and LCL, no significant relationship was found between antibody levels against a given oligosaccharide residue and clinical parameters such as age, leishmanin diameter, number of skin lesions, or time of evolution. It is noteworthy that 33% and 15% of MCL and LCL patients, respectively, did not have elevated antibody levels against the six different oligosaccharide residues studied. This suggests the presence of a subpopulation of non-humoral immunoreactive ACL patients. The relationship between abnormal levels of oligosaccharide antibodies and the final outcome of the disease remains to be established.

  NCBI PubMed ID: 1524141
  Journal NLM ID: 0370507
  Publisher: Northbrook, IL: American Society of Tropical Medicine and Hygiene
  Institutions: Instituto de Biomedicina, Caracas, Venezuela
  
   
  
  Leishmania major
  CSDB ID 101600 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_130701,IEDB_131187,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_140630,IEDB_141794,IEDB_141806,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_241101,IEDB_423153,IEDB_983930,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_44,SB_67,SB_7,SB_72,SB_88

• Article ID: 1967
  Rao AS, Roy N, Nimmich W "Structural studies on Klebsiella type 61 capsular polysaccharide" - Carbohydrate Research 67(2) (1978) 449-456
  

  The capsular polysaccharide from klebsiella type 61 was found to contain d-galactose, d-glucose, d-mannose, and d-glucuronic acid in the ratios 1:2:1:1. Acid hydrolysis of the polysaccharide gave one aldobiouronic acid, whose structure was established. Methylation analysis of the polysaccharide provided information about the linkages in the polysaccharide. The polysaccharide is composed of a pentasaccharide repeating unit for which structures are proposed.

  Publication DOI: 10.1016/S0008-6215(00)84132-4
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Macromolecules, Indian Association for the Cultivation of Science, Calcutta - 700032 India, Institut für Medizinische Mikrobiologie und Epidemiologie der Universität Rostock, DDR-25 Rostock GDR
  Methods: gel filtration, methylation, GLC-MS, sugar analysis, acid hydrolysis, GLC, carboxyl reduction, paper chromatography, ion-exchange chromatography, optical rotation measurement
  
   
  
  Klebsiella sp. K61
  CSDB ID 113348 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: K-antigen
Contained glycoepitopes: IEDB_115136,IEDB_130701,IEDB_131187,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_1394182,IEDB_140630,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_423153,IEDB_983930,SB_165,SB_166,SB_187,SB_195,SB_44,SB_67,SB_7,SB_72,SB_88

• Article ID: 2337
  Hungerer D, Jann K, Jann B, Orskov F, Orskov I "Immunochemistry of K antigens of Escherichia coli 4. The K antigen of E. coli O9:K30:H12" - European Journal of Biochemistry 2 (1967) 115-126
  
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  
   
  
  Escherichia coli K30
  CSDB ID 122381 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_131187,IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_144983,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_190606,IEDB_423153,IEDB_983930,SB_44,SB_7,SB_72

• Article ID: 3193
  Liu B, Senchenkova SN, Feng L, Perepelov AV, Xu T, Shevelev SD, Zhu Y, Shashkov AS, Zou M, Knirel YA, Wang L "Structural and molecular characterization of Shigella boydii type 16 O antigen" - Gene 380(1) (2006) 46-53
  

  Shigella is a well-known human pathogen causing dysentery and their typing is solely based on the O antigens. We investigated the chemical structure and gene cluster of Shigella boydii type 16 O antigen. As judged by sugar and methylation analyses along with NMR spectroscopy data, the O antigen has an O-acetylated branched pentasaccharide repeating O unit, which consists of two d-mannose residues (d-Man), one residue each of d-glucuronic acid (d-GlcA), N-acetylglucosamine (d-GlcNAc) and d-galactose (d-Gal), and the structure of the O unit was established. The O antigen gene cluster of S. boydii type 16 was identified and shown to contain putative genes for the synthesis of GDP-d-Man, genes encoding sugar transferases, O unit flippase (Wzx) and O antigen polymerase (Wzy) as expected. The function of the wzy gene was characterized by mutation test. Genes specific to S. boydii type 16 O antigen gene cluster were identified by screening 186 Escherichia coli and Shigella type strains, and can be used to develop PCR assays for detection of type 16 strains.

  O antigen gene cluster, S. boydii type 16, O antigen polymerase gene (wzy)

  NCBI PubMed ID: 16859842
  Journal NLM ID: 7706761
  Publisher: Amsterdam: Elsevier
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, TEDA School of Biological Sciences and Biotechnology, Nankai University, 23# HongDa Street, TEDA, Tianjin 300457, P.R. China, Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, 23# HongDa Street, TEDA, Tianjin 300457, P.R. China, Tianjin Biochip Corporation, 23# HongDa Street, TEDA, Tianjin 300457, P.R. China
  Methods: NMR, SDS-PAGE, chemical analysis, genetic methods
  
   
  
  Shigella boydii 16 G1219
  CSDB ID 20215 (all data & tools)
• Article ID: 5760
  Dobrochaeva K, Khasbiulina N, Shilova N, Antipova N, Obukhova P, Galanina O, Blixt O, Kunz H, Filatov A, Knirel Y, Le Pendu J, Khaidukov S, Bovin N "Specificity of human natural antibodies referred to as anti-Tn" - Molecular Immunology 120 (2020) 74-82
  

  To understand the role of human natural IgM known as antibodies against the carbohydrate epitope Tn, the antibodies were isolated using GalNAcα-Sepharose affinity chromatography, and their specificity was profiled using microarrays (a glycan array printed with oligosaccharides and bacterial polysaccharides, as well as a glycopeptide array), flow cytometry, and inhibition ELISA. The antibodies bound a restricted number of GalNAcα-terminated oligosaccharides better than the parent monosaccharide, e.g., 6-O-Su-GalNAcα and GalNAcα1-3Galβ1-3(4)GlcNAcβ. The binding with several bacterial polysaccharides that have no structural resemblance to the affinity ligand GalNAcα was quite unexpected. Given that GalNAcα is considered the key fragment of the Tn antigen, it is surprising that these antibodies bind weakly GalNAcα-OSer and do not bind a wide variety of GalNAcα-OSer/Thr-containing mucin glycopeptides. At the same time, we have observed specific binding to cells having Tn-positive glycoproteins containing similar glycopeptide motifs in a conformationally rigid macromolecule. Thus, specific recognition of the Tn antigen apparently requires that the naturally occurring "anti-Tn" IgM recognize a complex epitope comprising the GalNAcα as an essential component and a fairly long amino acid sequence where the amino acids adjacent to GalNAcα do not contact the antibody paratope; i.e., the antibodies recognize a spatial epitope or a molecular pattern rather than a classical continuous sequence. In addition, we have not found any increase in the binding of natural antibodies when GalNAcα residues were clustered. These results may help in further development of anticancer vaccines based on synthetic Tn constructs.

  cancer, glycans, natural antibodies, anti-glycan antibodies, Tn antigen

  NCBI PubMed ID: 32087569
  Publication DOI: 10.1016/j.molimm.2020.02.005
  Journal NLM ID: 7905289
  Publisher: Elsevier
  Correspondence: professorbovin@yandex.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, Moscow, Russian Federation, Semiotik LLC, 16/10 Miklukho-Maklaya, Moscow, Russian Federation, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation, National Research University Higher School of Economics, Moscow, Russian Federation, Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark, Institut Fur Organische Chemie, Johannes Gutenberg-Universitat Mainz, Duesbergweg 10-14, D-55128, Mainz, Germany, Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, Russian Federation, University of Nantes, Inserm, U892 IRT UN, 8 Quai MonCousu, BP70721 Nantes, FR 44007, France
  Methods: ELISA, affinity chromatography, flow cytometry analysis, printed glycan array (PGA) analysis, FACS assay
  
   
  
  Shigella boydii 16
  CSDB ID 3979 (all data & tools)
• Article ID: 5766
  Furevi A, Stahle J, Muheim C, Gkotzis S, Udekwu KI, Daley DO, Widmalm G "Structural analysis of the O-antigen polysaccharide from Escherichia coli O188" - Carbohydrate Research 498 (2020) 108051
  

  The structure of the O-antigen from Escherichia coli reference strain O188 (E. coli O188:H10) has been investigated. The lipopolysaccharide shows a typical nonrandom modal chain-length distribution and the sugar and absolute configuration analysis revealed d-Man, d-Glc, d-GlcN and d-GlcA as major components. The structure of the O-specific polysaccharide was determined using one- and two-dimensional (1)H and (13)C NMR spectroscopy experiments, where inter-residue correlations were identified by (1)H,(13)C-heteronuclear multiple-bond correlation and (1)H,(1)H-NOESY experiments, which revealed that it consists of pentasaccharide repeating units with the following structure: Biosynthetic aspects and NMR analysis are consistent with the presented structure as the biological repeating unit. The O-antigen of Shigella boydii type 16 differs only in that it carries O-acetyl groups to ~50% at O6 of the branch-point mannose residues. A molecular model of the E. coli O188 O-antigen containing 20 repeating units extends ~100 A, which is similar to the height of the periplasmic portion of polysaccharide co-polymerase Wzz proteins that regulate the O-antigen chain length of lipopolysaccharides in the Wzx/Wzy biosynthetic pathway.

  Lipopolysaccharide, Escherichia coli, NMR spectroscopy, Shigella boydii

  NCBI PubMed ID: 33075674
  Publication DOI: 10.1016/j.carres.2020.108051
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, sugar analysis, GLC
  
   
  
  Shigella boydii 16
  CSDB ID 3660 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: acceptor protein
Contained glycoepitopes: IEDB_115576,IEDB_130701,IEDB_131187,IEDB_136104,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_140116,IEDB_141794,IEDB_141807,IEDB_141830,IEDB_142488,IEDB_143632,IEDB_144983,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_164174,IEDB_190606,IEDB_241100,IEDB_76933,IEDB_983930,IEDB_983931,SB_136,SB_192,SB_196,SB_197,SB_44,SB_67,SB_7,SB_72

• Article ID: 3259
  Wacker M, Feldman MF, Callewaert N, Kowarik M, Clarke BR, Pohl NL, Hernandez M, Vines ED, Valvano MA, Whitfield C, Aebi M "Substrate specificity of bacterial oligosaccharyltransferase suggests a common transfer mechanism for the bacterial and eukaryotic systems" - Proceedings of the National Academy of Sciences of the USA 103(18) (2006) 7088-7093
  

  The PglB oligosaccharyltransferase (OTase) of Campylobacter jejuni can be functionally expressed in Escherichia coli, and its relaxed oligosaccharide substrate specificity allows the transfer of different glycans from the lipid carrier undecaprenyl pyrophosphate to an acceptor protein. To investigate the substrate specificity of PglB, we tested the transfer of a set of lipid-linked polysaccharides in E. coli and Salmonella enterica serovar Typhimurium. A hexose linked to the C-6 of the monosaccharide at the reducing end did not inhibit the transfer of the O antigen to the acceptor protein. However, PglB required an acetamido group at the C-2. A model for the mechanism of PglB involving this functional group was proposed. Previous experiments have shown that eukaryotic OTases have the same requirement, suggesting that eukaryotic and prokaryotic OTases catalyze the transfer of oligosaccharides by a conserved mechanism. Moreover, we demonstrated the functional transfer of the C. jejuni glycosylation system into S. enterica. The elucidation of the mechanism of action and the substrate specificity of PglB represents the foundation for engineering glycoproteins that will have an impact on biotechnology.

  LPS, glycoproteins, glycoengineering, PglB, Stt3p

  NCBI PubMed ID: 16641107
  Publication DOI: 10.1073/pnas.0509207103
  Journal NLM ID: 7505876
  Publisher: National Academy of Sciences
  Institutions: Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, CH-8093 Zurich, Switzerland, Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1, Department of Chemistry and Plant Sciences Institute, Gilman Hall, Iowa State University, Ames, IA 50011-3111, Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada N6A 5C1
  Methods: MS
  
   
  
  Escherichia coli O9:K30
  CSDB ID 20383 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_131187,IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_144983,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_190606,IEDB_423153,IEDB_983930,SB_44,SB_7,SB_72

• Article ID: 3505
  Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, Reeves P, Wang L "Structure and genetics of Shigella O antigens" - FEMS Microbiology Reviews 32(4) (2008) 627-653
  

  This review covers the O antigens of the 46 serotypes of Shigella, but those of most Shigella flexneri are variants of one basic structure, leaving 34 Shigella distinct O antigens to review, together with their gene clusters. Several of the structures and gene clusters are reported for the first time and this is the first such group for which structures and DNA sequences have been determined for all O antigens. Shigella strains are in effect Escherichia coli with a specific mode of pathogenicity, and 18 of the 34 O antigens are also found in traditional E. coli. Three are very similar to E. coli O antigens and 13 are unique to Shigella strains. The O antigen of Shigella sonnei is quite atypical for E. coli and is thought to have transferred from Plesiomonas. The other 12 O antigens unique to Shigella strains have structures that are typical of E. coli, but there are considerably more anomalies in their gene clusters, probably reflecting recent modification of the structures. Having the complete set of structures and genes opens the way for experimental studies on the role of this diversity in pathogenicity.

  structure, O antigen, Shigella, O antigen gene cluster, O antigen diversity

  NCBI PubMed ID: 18422615
  Publication DOI: 10.1111/j.1574-6976.2008.00114.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: wanglei@nankai.edu.cn
  Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China.
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, serological methods, genetic methods, biochemical methods
  
   
  
  Shigella boydii B16
  CSDB ID 23058 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_131187,IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_137485,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144983,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_190606,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_7,SB_72

• Article ID: 4430
  Ovodov YS "Bacterial capsular antigens. Structural patterns of capsular antigens" - Biochemistry (Moscow) 71(9) (2006) 937-954
  

  Structural patterns of bacterial capsular antigens including capsular polysaccharides and exoglycans are given in this review. In addition, the immunological activity of capsular antigens and their role in type specificity of bacteria are discussed.

  structure, capsular polysaccharides, bacterial capsular antigens, bacterial exoglycans, immunological activity, type specificity

  NCBI PubMed ID: 17009947
  Publication DOI: 10.1134/S000629790609001X
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: ovoys@physiol.komisc.ru
  Institutions: Institute of Physiology, Komi Science Center, Urals Branch of the Russian Academy of Sciences, Syktyvkar 167982, Russia
  
   
  
  Clostridium perfringens Hobbs 5
  CSDB ID 28771 (all data & tools)

Show legend Show as text

Structure type: structural motif or average structure
Contained glycoepitopes: IEDB_130701,IEDB_131187,IEDB_136044,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_152214,IEDB_174333,IEDB_190606,IEDB_983930,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_44,SB_67,SB_7,SB_72,SB_86,SB_88

• Article ID: 5638
  Ravenscroft N, Walker SG, Dutton GG, Smit J "Identification, isolation, and structural studies of extracellular polysaccharides produced by Caulobacter crescentus" - Journal of Bacteriology 173(18) (1991) 5677-5684
  

  Caulobacters are adherent prosthecate bacteria that are members of bacterial biofouling communities in many environments. Investigation of the cell surface carbohydrates produced by two strains of the freshwater Caulobacter crescentus, CB2A and CB15A, revealed a hitherto undetected extracellular polysaccharide (EPS) or capsule. Isolation and characterization of the EPS fractions showed that each strain produced a unique neutral EPS which could not be readily removed from the cell surface by washing. Monosaccharide analysis showed that the main CB2A EPS contained D-glucose, D-gulose, and D-fucose in a ratio of 3:1:1, whereas the CB15A EPS fraction contained D-galactose, D-glucose, D-mannose, and D-fucose in approximately equal amounts. Methylation analysis of the main CB2A EPS showed the presence of terminal glucose and gulose groups, 3-linked fucosyl, and two 3,4-linked glucosyl units, thus confirming the pentasaccharide repeating unit indicated by 1H nuclear magnetic resonance analysis. Similar studies of the CB15A EPS revealed a tetrasaccharide repeating unit consisting of terminal galactose, 4-linked fucosyl, 3-linked glucosyl, and 3,4-linked mannosyl residues. EPS was not detectable by thin-section electron microscopy techniques, including some methods designed to preserve or enhance capsules, nor was the EPS readily detected on the cell surface by scanning electron microscopy when conventional fixation techniques were used; however, a structure consistent with EPS was revealed when samples were prepared by cryofixation and freeze-substitution methods

  exopolysaccharides, gulose, Caulobacter crescentus

  NCBI PubMed ID: 1885545
  Publication DOI: 10.1128/jb.173.18.5677-5684.1991
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Institutions: Department of Chemistry, University of British Columbia, Vancouver, Canada, Department of Microbiology, University of British Columbia, Vancouver, Canada
  Methods: 1H NMR, methylation, GC-MS, acid hydrolysis, GC, Smith degradation, methanolysis, enzymatic digestion, colorimetry, periodate oxidation, acetylation, SEC, reduction, cell growth, dialysis, phenol-sulfuric acid assay, SEM, derivatization, evaporation, TEM, centrifugation
  
   
  
  Caulobacter crescentus CB15A
  CSDB ID 47872 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit ; n=20
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_131187,IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_144983,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_190606,IEDB_423153,IEDB_983930,SB_44,SB_7,SB_72

• Article ID: 5766
  Furevi A, Stahle J, Muheim C, Gkotzis S, Udekwu KI, Daley DO, Widmalm G "Structural analysis of the O-antigen polysaccharide from Escherichia coli O188" - Carbohydrate Research 498 (2020) 108051
  

  The structure of the O-antigen from Escherichia coli reference strain O188 (E. coli O188:H10) has been investigated. The lipopolysaccharide shows a typical nonrandom modal chain-length distribution and the sugar and absolute configuration analysis revealed d-Man, d-Glc, d-GlcN and d-GlcA as major components. The structure of the O-specific polysaccharide was determined using one- and two-dimensional (1)H and (13)C NMR spectroscopy experiments, where inter-residue correlations were identified by (1)H,(13)C-heteronuclear multiple-bond correlation and (1)H,(1)H-NOESY experiments, which revealed that it consists of pentasaccharide repeating units with the following structure: Biosynthetic aspects and NMR analysis are consistent with the presented structure as the biological repeating unit. The O-antigen of Shigella boydii type 16 differs only in that it carries O-acetyl groups to ~50% at O6 of the branch-point mannose residues. A molecular model of the E. coli O188 O-antigen containing 20 repeating units extends ~100 A, which is similar to the height of the periplasmic portion of polysaccharide co-polymerase Wzz proteins that regulate the O-antigen chain length of lipopolysaccharides in the Wzx/Wzy biosynthetic pathway.

  Lipopolysaccharide, Escherichia coli, NMR spectroscopy, Shigella boydii

  NCBI PubMed ID: 33075674
  Publication DOI: 10.1016/j.carres.2020.108051
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, sugar analysis, GLC
  
   
  
  Escherichia coli O188:H10
  CSDB ID 32099 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: teichuronic acid
Contained glycoepitopes: IEDB_115136,IEDB_131187,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_232584,IEDB_423153,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_7,SB_72

• Article ID: 5841
  Shashkov AS, Tul'skaya EM, Streshinskaia GM, Dmitrenok AS, Potekhina NV, Senchenkova SN, Piskunkova NF, Dorofeeva LV, Evtushenko LI "Rhamnomannans and Teichuronic Acid from the Cell Wall of Rathayibacter tritici VKM Ac-1603T" - Biochemistry (Moscow) 85(3) (2020) 369-377
  

  The structures of three cell wall glycopolymers of the phytopathogen Rathayibacter tritici VKM Ac-1603T (family Microbacteriaceae, order Micrococcales, class Actinobacteria) were established by chemical methods and NMR spectroscopy. Polymer 1 is a branched rhamnomannan with the repeating unit →3)-α-[β-D-Xylp-(1→2)]-D-Manp-(1→2)-α-D-Rhap-(1→3)-α-D-Manp-(1→2)-α-D-Rhap-(1→; polymer 2 is a linear rhamnomannan with the repeating unit →2)-α-D-Manp-(1→2)-α-D-Rhap-(1→3)-α-D-Manp-(1→2)-α-D-Rhap-(1→; polymer 3 is a branched teichuronic acid containing monosaccharide residues GlcA, Gal, Man, and Glc at a 1 : 1 : 1 : 5 ratio (see the text for the structures). It has been demonstrated that representatives of four Rathayibacter species studied to date (R. tritici VKM Ac-1603T, R. iranicus VKM Ac-1602 T, R. toxicus VKM Ac-1600 and "Rathayibacter tanaceti" VKM Ac-2596) contain differing patterns of phosphate-free glycopolymers. At the same time, the above Rathayibacter strains have a common property - the presence of rhamnomannans with D-rhamnose. These rhamnomannans may be linear or branched and differing in the positions of glycosidic bonds and side substituents. The presence in the cell wall of rhamnomannans with D-rhamnose may serve as useful chemotaxonomic marker of the genus Rathayibacter.

  NMR spectroscopy, cell wall, teichuronic acid, D-rhamnose, Rathayibacter, rhamnomannan

  NCBI PubMed ID: 32564741
  Publication DOI: 10.1134/S0006297920030128
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: em_tulskaya@mail.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia, Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, acid hydrolysis, GLC, anion-exchange chromatography, paper chromatography, composition analysis, paper electrophoresis
  
   
  
  Rathayibacter tritici VKM Ac-1603(T)
  CSDB ID 32196 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-linked glycoprotein
Contained glycoepitopes: IEDB_130701,IEDB_131187,IEDB_136104,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_143632,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_983930,SB_136,SB_196,SB_44,SB_67,SB_7,SB_72

• Article ID: 6445
  Neustroev KN, Golubev AM, Ibatullin FM, Moseichuk AV "Microheterogeneity in O-type sugar chains of carbohydrases secreted by Asp. awamori" - Biochemistry and Molecular Biology International 30 (1993) 107-113
  

  This paper deals with microheterogeneity in the structure of O-linked sugars of carbohydrases secreted by Asp. awamori, namely glucoamylase, α-galactosidase and α-glucosidase. Microheterogeneity was found to be related both to post-secretion deglycosylation and to changes in transferase activity induced by the differences in culturing conditions.

  NCBI PubMed ID: 8358322
  Journal NLM ID: 9306673
  Institutions: Dept. of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russia
  
   
  
  Aspergillus awamori
  CSDB ID 106490 (all data & tools)

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Structure type: oligomer
Aglycon: (->3) Ser/Thr-peptide
Trivial name: O-glycan
Compound class: glycoprotein
Contained glycoepitopes: IEDB_130701,IEDB_131187,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_1394182,IEDB_141793,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_153220,IEDB_190606,IEDB_983930,SB_198,SB_44,SB_67,SB_7,SB_72

• Article ID: 6953
  Goto M "Protein O-Glycosylation in Fungi: Diverse Structures and Multiple Functions" - Bioscience, Biotechnology, and Biochemistry 71(6) (2007) 1415-1427
  

  Protein glycosylation is essential for eukaryotic cells from yeasts to humans. When compared to N-glycosylation, O-glycosylation is variable in sugar components and the mode of linkages connecting the sugars. In fungi, secretory proteins are commonly mannosylated by protein O-mannosyltransferase (PMT) in the endoplasmic reticulum, and subsequently glycosylated by several glycosyltransferases in the Golgi apparatus to form glycoproteins with diverse O-glycan structures. Protein O-glycosylation has roles in modulating the function of secretory proteins by enhancing the stability and solubility of the proteins, by affording protection from protease degradation, and by acting as a sorting determinant in yeasts. In filamentous fungi, protein O-glycosylation contributes to proper maintenance of fungal morphology, hyphal development, and differentiation. This review describes recent studies of the structure and function of protein O-glycosylation in industrially and medically important fungi.

  O-glycosylation, Aspergillus, protein O-mannosyltransferase

  NCBI PubMed ID: 17587671
  Publication DOI: 10.1271/bbb.70080
  Journal NLM ID: 9205717
  Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry
  Correspondence: m_goto@agr.kyushu-u.ac.jp
  Institutions: Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Japan
  
   
  
  Aspergillus niger, Aspergillus awamori X-100
  CSDB ID 42208 (all data & tools)