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_137485,IEDB_1391961,IEDB_141584,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_152206,IEDB_152214,IEDB_174333,IEDB_885822,IEDB_983930,SB_44,SB_67,SB_72,SB_86

• Article ID: 381
  Skurnik M, Zhang L "Molecular genetics and biochemistry of Yersinia lipopolysaccharide" - APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica 104(12) (1996) 849-872
  

  Studies on the molecular genetics of bacterial LPS serve at least two main purposes: (i) to help develop an understanding of the biology, biochemistry and genetics of this bacterial surface macromolecule, and (ii) to provide a basis for both vaccine development and virulence experiments. Both of these goals have been the driving force in studies of Yersinia LPS carried out during the last decade. Here we will review the progress made in the molecular genetics and biochemistry of Yersinia LPS. A deep understanding has been achieved with respect to Y. enterocolitica serotype O:3, reaching as far as a detailed analysis of the gene clusters directing the biosynthesis of the outer core oligosaccharide and of the O-ag. The O-ag gene clusters of Y. enterocolitica serotype O:8 and Y. pseudotuberculosis serotypes O:2a and O:5a have also been cloned and partially characterized LPS biosynthesis of these Yersinia species includes examples of the two major variations recognized in the biosynthesis of this macromolecule: (i) homopolymeric or O-antigen polymerase-independent biosynthesis, and (ii) heteropolymeric or O-antigen polymerase-dependent biosynthesis.

  Lipopolysaccharide, genetic, gene, genetics, O-antigen, biochemistry, Yersinia, molecular genetics

  NCBI PubMed ID: 9048864
  Publication DOI: 10.1111/j.1699-0463.1996.tb04951.x
  Journal NLM ID: 8803400
  Publisher: Copenhagen: Munksgaard
  Institutions: Turku Centre for Biotechnology, University of Turku, Finland, department of Medical Microbiology, University of Turku, Turku, Finland
  
   
  
  Yersinia pseudotuberculosis O5a
  CSDB ID 31543 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Trivial name: O-unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_2189046

• Article ID: 1452
  Chatterjee SN, Chaudhuri K "Lipopolysaccharides of Vibrio cholerae. I. Physical and chemical characterization" - Biochimica et Biophysica Acta 1639(2) (2003) 65-79
  

  Vibrio cholerae is the causative organism of the disease cholera. The lipopolysaccharide (LPS) of V. cholerae plays an important role in eliciting the antibacterial immune response of the host and in classifying the vibrios into some 200 or more serogroups. This review presents an account of our up-to-date knowledge of the physical and chemical characteristics of the three constituents, lipid-A, core-polysaccharide (core-PS) and O-antigen polysaccharide (O-PS), of the LPS of V. cholerae of different serogroups including the disease-causing ones, O1 and O139. The structure and occurrence of the capsular polysaccharide (CPS) on V. cholerae O139 have been discussed as a relevant topic. Similarity and dissimilarity between the structures of LPS of different serogroups, and particularly between O22 and O139, have been analysed with a view to learning their role in the causation of the epidemic form of the disease by avoiding the host defence mechanism and in the evolution of the newer pathogenic strains in future. An idea of the emerging trends of research involving the use of immunogens prepared from synthetic oligosaccharides that mimic terminal epitopes of the O-PS of V. cholerae O1 in the development of a conjugate anti cholera vaccine is also discussed.

  Lipopolysaccharide, structure, lipid A, capsular polysaccharide, serogroup, Vibrio cholerae

  NCBI PubMed ID: 14559113
  Publication DOI: 10.1016/j.bbadis.2003.08.004
  Journal NLM ID: 0217513
  Publisher: Elsevier
  Correspondence: sncac@sify.com (S.N. Chatterjee)
  Institutions: Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Sector-1, Calcutta-700 064, India, Biophysics Division, Indian Institute of Chemical Biology, Jadavpur, Calcutta-700 032, India
  
   
  
  Vibrio cholerae O3
  CSDB ID 31697 (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
  
   
  
  Vibrio cholerae O3
  CSDB ID 27769 (all data & tools)
• Article ID: 4979
  Chowdhury TA, Jansson PE, Lindberg B, Lindberg J, Gustafsson B, Holme T "Structural studies of the Vibrio cholerae O:3 O-antigen polysaccharide" - Carbohydrate Research 215(2) (1991) 303-314
  

  The structure of the Vibrio cholerae O:3 O-antigen polysaccharide has been investigated, mainly by n.m.r. spectroscopy, mass spectrometry, sugar and methylation analysis, and specific degradations, and is proposed to involve the following tetrasaccharide repeating-unit. [formula: see text]. In this structure, D-D-Hep is D-glycero-D-manno-heptose, Asc is 3,6-dideoxy-L-arabino-hexose (ascarylose), and Sug is 2,4-diamino-2,4,6-trideoxy-D-glucose (bacillosamine) in which N-2 is acetylated and N-4 is acylated with a 3,5-dihydroxyhexanoic acid. That the 2,4-diamino-2,4,6-trideoxy-D-glucose residue is linked through O-3 and not through one of the hydroxyl groups in the 3,5-dihydroxyhexanoyl group is indicated but not definitely proved. The configuration of the latter group has not been determined. The f.a.b.-mass spectrum of the methylated O-antigen indicates that the structure given above also represents the biological repeating-unit.

  NMR, O-antigen, Vibrio cholerae

  NCBI PubMed ID: 1794128
  Publication DOI: 10.1016/0008-6215(91)84029-E
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, methylation, GLC-MS, gel filtration, NMR-2D, partial acid hydrolysis, sugar analysis, methanolysis
  
   
  
  Vibrio cholerae O3
  CSDB ID 298 (all data & tools)

Show legend Show as text

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

• Article ID: 1778
  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
  
   
  
  Yersinia pseudotuberculosis VA
  CSDB ID 108440 (all data & tools)
• Article ID: 2370
  Gorshkova RP, Korchahina NI, Ovodov YS "Structural studies on the O-specific side-chain polysaccharide of lipopolysaccharide from the Yersinia pseudotuberculosis VA serovar" - European Journal of Biochemistry 131(2) (1983) 345-347
  

  The polysaccharide of the O-specific side chain of the lipopolysaccharide from the Yersinia pseudotuberculosis VA serovar has been isolated and studied. The structural pattern of the chemical repeating unit of the specific polysaccharide has been proposed as follows: (formula; see text).

  NCBI PubMed ID: 6832155
  Publication DOI: 10.1111/j.1432-1033.1983.tb07268.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Pacific Institute of Bioorganic Chemistry, Far East Science Centre, Academy of Sciences of the U.S.S.R., Vladivostok
  Methods: GLC-MS, IR
  
   
  
  Yersinia pseudotuberculosis VA
  CSDB ID 122710 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_2189046

• Article ID: 1778
  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
  
   
  
  Vibrio cholerae O3
  CSDB ID 108551 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_130701,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_141798,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 2728
  Bruse GW, Wollin R, Lindberg AA "Interaction between phage G13 and its oligosaccharide receptor studied by equilibrium dialysis" - Journal of Molecular Recognition 2 (1989) 18-24
  
  Journal NLM ID: 9004580
  Publisher: Chichester, Sussex, UK: John Wiley & Sons
  
   
  
  Salmonella typhimurium SH4809
  CSDB ID 140661 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: O(CH2)8COOMe
Contained glycoepitopes: IEDB_130701,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 2030
  Bock K, Meldal M, Bundle DR, Iversen T, Pinto BM, Garegg PJ, Kvanström I, Norberg T, Lindberg AA, Svenson SB "The conformation of Salmonella O-antigenic oligosaccharides of serogroups A, B, and D1 inferred from 1H- and 13C-nuclear magnetic resonance spectroscopy" - Carbohydrate Research 130 (1984) 35-53
  

  The conformational model derived by the HSEA calculation method was used to interpret the n.m.r. data for solutions of oligosaccharides corresponding to the Salmonella serogroups A, B, and D1 antigenic determinants. The favored conformer, derived by calculation, accounted for the observed, chemical-shift changes and accurately predicted the existence and magnitude of inter-ring proton n.O.e.'s. Extensive proton-density and compression of proton, Van der Waals radii were correlated with deshielding of specific proton-resonances. The model of lipopolysaccharide conformation accounts for the known antigenic properties of Salmonella O-antigens.

  NCBI PubMed ID: 6478461
  Publication DOI: 10.1016/0008-6215(84)85268-4
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, University of Stockholm, Stockholm, Sweden, Division of Biological Sciences, National Research Council of Canada, Ottawa, Ontario K1A OR6 Canada, Department of Bacteriology, National Bacteriological Laboratory, S-105 21 Stockholm, Sweden, Department of Organic Chemistry, The Technical University of Denmark, 2800 Lyngby Denmark
  Methods: 13C NMR, 1H NMR, conformation analysis, nOe, HSEA
  
   
  
  Salmonella sp. A, Salmonella sp. B, Salmonella sp. D1
  CSDB ID 114212 (all data & tools)

Show legend Show as text

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

• Article ID: 3841
  De Castro C, Parrilli M, Holst O, Molinaro A "Microbe-associated molecular patterns in innate immunity. Extraction and chemical analysis of Gram-negative bacterial lipopolysaccharides" - Methods in Enzymology 480 (2010) 89-115
  

  Bacterial lipopolysaccharides (LPSs) are the major component of the outer membrane of Gram-negative bacteria. They have a structural role since they contribute to the cellular rigidity by increasing the strength of cell wall and mediating contacts with the external environment that can induce structural changes to allow life in different conditions. Furthermore, the low permeability of the outer membrane acts as a barrier to protect bacteria from host-derived antimicrobial compounds. They also have a very important role in the elicitation of the animal and plant host innate immunity since they are microbe-associated molecular patterns, namely, they are glycoconjugates produced only by Gram-negative bacteria and are recognized as a molecular hallmark of invading microbes. LPSs are amphiphilic macromolecules generally comprising three defined regions distinguished by their genetics, structures, and function: the lipid A, the core oligosaccharide and a polysaccharide portion, the O-chain. In some Gram-negative bacteria, LPS can terminate with the core portion to form rough-type LPS (R-LPS, LOS). In this chapter, we will describe the isolation of both kinds of LPSs and their full chemical analysis, pivotal operations in the complete description of the primary structure of such important glycoconjugates.

  lipopolysaccharides, isolation, gram negative bacteria, methods, MS, chemical analysis

  NCBI PubMed ID: 20816206
  Publication DOI: 10.1016/S0076-6879(10)80005-9
  Journal NLM ID: 0212271
  Correspondence: mikael.skurnik@helsinki.fi
  Institutions: Universita di Napoli Federico II, Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte Santangelo, Via Cynthia, Napoli, Italy
  Methods: 13C NMR, 1H NMR, NMR-2D, PCR, NMR-1D, genetic methods
  
   
  
  Yersinia pseudotuberculosis O5a
  CSDB ID 25593 (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
  
   
  
  Yersinia pseudotuberculosis O5a
  CSDB ID 27627 (all data & tools)
• Article ID: 5010
  Kenyon JJ, Cunneen MM, Reeves PR "Genetics and evolution of Yersinia pseudotuberculosis O-specific polysaccharides: a novel pattern of O-antigen diversity" - FEMS Microbiology Reviews 41(2) (2017) 200-217
  

  O-antigen polysaccharide is a major immunogenic feature of the lipopolysaccharide of Gram-negative bacteria, and most species produce a large variety of forms that differ substantially from one another. There are 18 known O-antigen forms in the Yersinia pseudotuberculosis complex, which are typical in being composed of multiple copies of a short oligosaccharide called an O unit. The O-antigen gene clusters are located between the hemH and gsk genes, and are atypical as 15 of them are closely related, each having one of five downstream gene modules for alternative main-chain synthesis, and one of seven upstream modules for alternative side-branch sugar synthesis. As a result, many of the genes are in more than one gene cluster. The gene order in each module is such that, in general, the earlier a gene product functions in O-unit synthesis, the closer the gene is to the 5 end for side-branch modules or the 3 end for main-chain modules. We propose a model whereby natural selection could generate the observed pattern in gene order, a pattern that has also been observed in other species.

  Lipopolysaccharide, serotype, O antigen, gene cluster, O-specific polysaccharide, Yersinia pseudotuberculosis, O-antigen polysaccharide

  NCBI PubMed ID: 28364730
  Publication DOI: 10.1093/femsre/fux002
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: peter.reeves@sydney.edu.au
  Institutions: School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia, Institute of Health and Biomedical Innovation, Queensland University of Technology. Brisbane, QLD 4001, Australia
  Methods: function analysis of gene clusters
  
   
  
  Yersinia pseudotuberculosis O5a
  CSDB ID 12125 (all data & tools)

Show legend Show as text

Structure type: monomer
Trivial name: ascarylose

• Article ID: 4176
  Thorson JS, Lo SF, Liu HW "Molecular basis of 3,6-dideoxyhexose biosynthesis: Elucidation of CDP-ascarylose biosynthetic genes and their relationship to other 3,6- dideoxyhexose pathways" - Journal of the American Chemical Society 115 (1993) 5827-5828
  
  Journal NLM ID: 7503056
  Publisher: American Chemical Society
  
   
  
  (Enterobacteriaceae)
  CSDB ID 131498 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_2189046

• Article ID: 4554
  Kokoulin MS, Kalinovsky AI, Komandrova NA, Tovarchi VE, Tomshich SV, Nedashkovskaya OI, Vaskovsky VE "The structure of the O-specific polysaccharide from marine bacterium Litorimonas taeanensis G5 containing 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-D-quinovose and 2-acetamido-2,6-dideoxy-L-xylo-hexos-4-ulose" - Carbohydrate Research 375 (2013) 105-111
  

  The O-polysaccharide was isolated from the lipopolysaccharide of Litorimonas taeanensis G5T and studied by chemical methods along with 1H and 13C NMR spectroscopy, including 1H, 1H COSY, 1D and 2D TOCSY, NOESY, 1H, 13C HSQC, HMBC, and H2BC experiments. The following new structure of the O-polysaccharide of L. taeanensis G5T containing 2-acetamido-2-deoxy-d-galacturonic acid (d-GalNAcA), 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-d-quinovose (d-QuiNAc4NR), and 2-acetamido-2,6-dideoxy-l-xylo-hexos-4-ulose (l-Sug) was established: where R is (3S,5S)-3,5-dihydroxyhexanoic acid.

  O-specific polysaccharide, 2-acetamido-2, 6-dideoxy-L-xylo-hexos-4-ulose, 2-Acetamido-4-((3S, 5S)-3, 5-dihydroxyhexanamido)-2, 4-dideoxy-D-quinovose, Litorimonas taeanensis

  NCBI PubMed ID: 23694711
  Publication DOI: 10.1016/j.carres.2013.04.004
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: maxchem@mail.ru
  Institutions: G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
  Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, NMR-1D, triflic acid solvolysis, borohydride reduction
  
   
  
  Vibrio cholerae O3
  CSDB ID 29613 (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_130648,IEDB_137473,IEDB_140630,IEDB_141807,IEDB_151531,IEDB_153510,IEDB_423153

• Article ID: 4780
  Ovchinnikova OG, Moryl M, Shashkov AS, Chizhov AO, Arbatsky NP, Shpirt AM, Rozalski A, Knirel YA "Structure of the O-polysaccharide of Providencia alcalifaciens O2 containing ascarylose and N-(L-alanyl)-D-glucosamine" - Carbohydrate Research 401 (2015) 11-15
  

  The O-polysaccharide was obtained by degradation of the lipopolysaccharide of Providencia alcalifaciens O2 under mild acidic conditions followed by GPC. The polysaccharide was found to contain two unusual components: 3,6-dideoxy-L-arabino-hexose (ascarylose, Asc) and 2-(L-alanyl)amino-2-deoxy-D-glucose (GlcNAla). Ascarylose was partially split off during lipopolysaccharide degradation and could be eliminated completely by selective acid hydrolysis, which also partially cleaved the β-GAlNAc-(1→6) linkage. The following structure of the branched pentasaccharide repeating unit was established by (1)H and (13)C NMR spectroscopy of the O-polysaccharide and O-deacetylated polysaccharide, as well as products of partial acid hydrolysis: α-Ascp-(1→4)-α-D-GlcpA-(1→4)→6)-β-D-GlcpNAla-(1→4)-β-D-GlpA-(1→3)-β-D-GalpNAc-(1→ ~60% OAc--3).

  Lipopolysaccharide, O-antigen, Providencia alcalifaciens, bacterial polysaccharide structure, Ascarylose

  NCBI PubMed ID: 25464076
  Publication DOI: 10.1016/j.carres.2014.10.016
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: yknirel@gmail.com (Y.A. Knirel)
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Łódź, PL 90-237 Łódź, Poland
  Methods: 13C NMR, 1H NMR, NMR-2D, partial acid hydrolysis, ESI-MS, GLC, de-O-acetylation, composition analysis, methanolysis, GPC, mild acid degradation
  
   
  
  Providencia alcalifaciens O2:H2 (67002)
  CSDB ID 30646 (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_130648,IEDB_137473,IEDB_140630,IEDB_141807,IEDB_151531,IEDB_153510,IEDB_423153

• Article ID: 4780
  Ovchinnikova OG, Moryl M, Shashkov AS, Chizhov AO, Arbatsky NP, Shpirt AM, Rozalski A, Knirel YA "Structure of the O-polysaccharide of Providencia alcalifaciens O2 containing ascarylose and N-(L-alanyl)-D-glucosamine" - Carbohydrate Research 401 (2015) 11-15
  

  The O-polysaccharide was obtained by degradation of the lipopolysaccharide of Providencia alcalifaciens O2 under mild acidic conditions followed by GPC. The polysaccharide was found to contain two unusual components: 3,6-dideoxy-L-arabino-hexose (ascarylose, Asc) and 2-(L-alanyl)amino-2-deoxy-D-glucose (GlcNAla). Ascarylose was partially split off during lipopolysaccharide degradation and could be eliminated completely by selective acid hydrolysis, which also partially cleaved the β-GAlNAc-(1→6) linkage. The following structure of the branched pentasaccharide repeating unit was established by (1)H and (13)C NMR spectroscopy of the O-polysaccharide and O-deacetylated polysaccharide, as well as products of partial acid hydrolysis: α-Ascp-(1→4)-α-D-GlcpA-(1→4)→6)-β-D-GlcpNAla-(1→4)-β-D-GlpA-(1→3)-β-D-GalpNAc-(1→ ~60% OAc--3).

  Lipopolysaccharide, O-antigen, Providencia alcalifaciens, bacterial polysaccharide structure, Ascarylose

  NCBI PubMed ID: 25464076
  Publication DOI: 10.1016/j.carres.2014.10.016
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: yknirel@gmail.com (Y.A. Knirel)
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Łódź, PL 90-237 Łódź, Poland
  Methods: 13C NMR, 1H NMR, NMR-2D, partial acid hydrolysis, ESI-MS, GLC, de-O-acetylation, composition analysis, methanolysis, GPC, mild acid degradation
  
   
  
  Providencia alcalifaciens O2:H2 67002
  CSDB ID 30821 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-antigen
Contained glycoepitopes: IEDB_2189046

• Article ID: 5157
  Goyette-Desjardins G, Vinogradov E, Okura M, Takamatsu D, Gottschalk M, Segura M "Streptococcus suis serotype 3 and serotype 18 capsular polysaccharides contain di-N-acetyl-bacillosamine" - Carbohydrate Research 466 (2018) 18-29
  

  Streptococcus suis serotype 3 is counted among the S. suis serotypes causing clinical disease in pigs. Yet, limited information is available on this serotype. Here we determined for the first time the chemical composition and structure of serotype 3 capsular polysaccharide (CPS), a major bacterial virulence factor and the antigen at the origin of S. suis classification into serotypes. Chemical and spectroscopic data gave the repeating unit sequence for serotype 3: [4)D-GlcA (β1-3)d-QuiNAc4NAc(β1-]n. To the best of our knowledge, this is the first report of di-N-acetyl-d-bacillosamine (QuiNAc4NAc) containing polysaccharides in Streptococci and the second time this rare diamino sugar has been observed in a Gram-positive bacterial species since its initial report. This led to the identification of homologues of UDP-QuiNAc4NAc synthesis genes in S. suis serotype 18. Thus, the repeating unit sequence for serotype 18 is: [3)d-GalNAc(α1-3)[d-Glc (β1-2)]d-GalA4OAc(β1-3)d-GalNAc(α1-3)d-QuiNAc4NAc(α1-]n. A correlation between S. suis serotypes 3 and 18 CPS sequences and genes of these serotypes' cps loci encoding putative glycosyltransferases and polymerase responsible for the biosynthesis of the repeating unit was tentatively established. Knowledge of CPS structure and composition will contribute to better dissect the role of this bacterial component in the pathogenesis of S. suis serotypes 3 and 18.

  polysaccharide, capsular polysaccharide, polysaccharides, carbohydrate structure, Streptococcus suis, Di-N-Acetyl-bacillosamine, Serotype 18, Serotype 3

  NCBI PubMed ID: 30014879
  Publication DOI: 10.1016/j.carres.2018.07.003
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: mariela.segura@umontreal.ca
  Institutions: Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., St-Hyacinthe, Quebec, J2S 2M2, Canada, Canadian Glycomics Network (GlycoNet), University of Alberta, 11227 Saskatchewan Dr., Edmonton, Alberta, T6G 2G2, Canada, National Research Council, 100 Sussex Dr., Ottawa, Ontario, K1A 0R6, Canada, Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan, The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu, 501-1193, Japan
  Methods: 13C NMR, 1H NMR, periodate oxidation, gel filtration, NMR-2D, GC-MS, de-O-acylation, sugar analysis, methanolysis, SEC-MALS, bioinformatic analysis
  
   
  
  Vibrio cholerae O3
  CSDB ID 12601 (all data & tools)

Show legend Show as text

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

• Article ID: 6089
  Knirel YA, Anisimov AP, Kislichkina AA, Kondakova AN, Bystrova OV, Vagaiskaya AS, Shatalin KY, Shashkov AS, Dentovskaya SV "Lipopolysaccharide of the Yersinia pseudotuberculosis Complex" - Biomolecules 11(10) (2021) 1410
  

  Lipopolysaccharide (LPS), localized in the outer leaflet of the outer membrane, serves as the major surface component of the Gram-negative bacterial cell envelope responsible for the activation of the host's innate immune system. Variations of the LPS structure utilized by Gram-negative bacteria promote survival by providing resistance to components of the innate immune system and preventing recognition by TLR4. This review summarizes studies of the biosynthesis of Yersinia pseudotuberculosis complex LPSs, and the roles of their structural components in molecular mechanisms of yersiniae pathogenesis and immunogenesis.

  core, Pathogenesis, lipid A, Yersinia pseudotuberculosis, lipopolysaccharide (LPS), Yersinia pestis, Plague, pathogenicity factor

  NCBI PubMed ID: 34680043
  Publication DOI: 10.3390/biom11101410
  Journal NLM ID: 101596414
  Publisher: Basel, Switzerland: MDPI
  Correspondence: Y.A. Knirel ; S.V. Dentovskaya
  Institutions: Laboratory of Carbohydrate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Laboratory for Plague Microbiology, Especially Dangerous Infections Department, State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
  
   
  
  Yersinia pseudotuberculosis O5a
  CSDB ID 9641 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137473,IEDB_140630,IEDB_141807,IEDB_151531,IEDB_153510,IEDB_423153

• Article ID: 6301
  Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" - Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
  

  Bacterial surface glycans perform a diverse and important set of biological roles, and have been widely used in the treatment of bacterial infectious diseases. The majority of bacterial surface glycans are decorated with diverse rare functional groups, including amido, acetamidino, carboxamido and pyruvate groups. These functional groups are thought to be important constituents for the biological activities of glycans. Chemical synthesis of glycans bearing these functional groups or their variants is essential for the investigation of structure-activity relationships by a medicinal chemistry approach. To date, a broad choice of synthetic methods is available for targeting the different rare functional groups in bacterial surface glycans. This article reviews the structures of naturally occurring rare functional groups in bacterial surface glycans, and the chemical methods used for installation of these groups.

  chemical synthesis, acetamidino group, amido group, bacterial surface glycan, carboxamido group, pyruvyl ketal

  NCBI PubMed ID: 35750381
  Publication DOI: 10.1016/S1875-5364(22)60177-8
  Journal NLM ID: 101504416
  Publisher: Beijing: Science Press; Elsevier
  Correspondence: J. Yin
  Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
  
   
  
  Providencia alcalifaciens O2
  CSDB ID 21144 (all data & tools)