Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS, O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_174035,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 69
  Falt IC, Mills D, Schweda EKH, Timmis KN, Lindberg AA "Construction of recombinant aroA salmonellae stably producing the Shigella dysenteriae serotype 1 O-antigen and structural characterization of the Salmonella/Shigella hybrid LPS" - Microbial Pathogenesis 20(1) (1996) 11-30
  

  The TN501 mercury resistant transposon containing the rfp and rfb loci encoding biosynthesis of the O-antigen of Shigella dysenteriae serotype 1 lipopolysaccharide (LPS) was constructed and introduced into aroA mutants of Salmonella typhimurium and Salmonella dublin. In five recombinant strains, both homologous LPS and hybrid LPS, consisting of Salmonella lipid A-core and Shigella O-antigen, were produced. All derivatives but one (SL3235) stably inherited the new trait. Immunofluorescence microscopy, using mixtures of differentially-labelled antibodies specific for either the Salmonella or the Shigella O-antigen, demonstrated that individual bacteria produced both types of LPS. Qualitative and quantitative analysis of polysaccharides obtained by mild hydrolysis of purified LPS was carried out by methylation analysis and NMR spectroscopy, and revealed that the ratio of Salmonella to Shigella O-antigen repeating units in the high molecular weight fraction of isolated polysaccharides varied from 1.3: 1 to 8.4:1 as based on the relative proportions of 1,4,5-tri-O-acetyl-2,3-di-O-methyl-L-rhamnitol (Salmonella repeating unit) and 1,3,5-tri-O-acetyl-2,4-di-O-methyl-L-rhamnitol (Shigella repeating unit). The attachment site of the Shigella O-antigen to the Salmonella core was investigated by construction of a mutant rfp-rfb gene cluster encoding the synthesis of only one repeat unit of the Shigella dysenteriae type 1 O-antigen, and its introduction into a rough Salmonella strain. This hybrid organism produced a polysaccharide with the following structure, [formula: see text] demonstrating that the Shigella dysenteriae type 1 O-antigen is linked at position O-4 of the subterminal D-glucose unit in the Salmonella core

  LPS, Salmonella, Shigella dysenteriae type 1, hybrids, vaccine.

  NCBI PubMed ID: 8692007
  Journal NLM ID: 8606191
  Publisher: Academic Press
  Institutions: Department of Immunology, Microbiology, Pathology and Infectious Diseases, Karolinska Institute, Huddinge Hospital, Sweden, Department of Medical Biochemistry, University of Geneva, Switzerland, Division of Microbiology, National Research Centre for Biotechnology, Braunschweig, Germany, Clinical Research Centre, Karolinska Institute, Novum, Huddinge Hospital, Sweden
  
   
  
  Salmonella dublin
  CSDB ID 2156 (all data & tools)
• Article ID: 1369
  Baxa U, Steinbacher S, Miller S, Weintraub A, Huber R, Seckler R "Interactions of phage P22 tails with their cellular receptor, Salmonella O-antigen polysaccharide" - Biophysical Journal 71 (1996) 2040-2048
  

  Bacteriophage P22 binds to its cell surface receptor, the repetitive O-antigen structure in Salmonella lipopolysaccharide, by its six homotrimeric tailspikes. Receptor binding by soluble tailspikes and the receptor-inactivating endorhamnosidase activity of the tailspike protein were studied using octa- and dodecasaccharides comprising two and three O-antigen repeats of Salmonella enteritidis and Salmonella typhimurium lipopolysaccharides. Wild-type tailspike protein and three mutants (D392N, D395N, and E359Q) with defective endorhamnosidase activity were used. Oligosaccharide binding to all three subunits, measured by a tryptophan fluorescence quench or by fluorescence depolarization of a coumarin label attached to the reducing end of the dodecasaccharide, occurs independently. At 10 degrees C, the binding affinities of all four proteins to oligosaccharides from both bacterial strains are identical within experimental error, and the binding constants for octa- and dodecasaccharides are 1 x 10(6) M(-1) and 2 x 10(6) M(-1), proving that two O-antigen repeats are sufficient for lipopolysaccharide recognition by the tailspike. Equilibration with the oligosaccharides occurs rapidly, but the endorhamnosidase produces only one cleavage every 100 s at 10 degrees C or about 2 min(-1) at the bacterial growth temperature. Thus, movement of virions in the lipopolysaccharide layer before DNA injection may involve the release and rebinding of individual tailspikes rather than hydrolysis of the O-antigen.

  polysaccharide, O-antigen, O antigen, Salmonella, interaction, cellular, receptor, phage

  NCBI PubMed ID: 8889178
  Journal NLM ID: 0370626
  Publisher: Cambridge, MA: Cell Press
  Correspondence: robert.seckler@biologie.uniregensburg.de
  Institutions: Universitat Regensberg, Phusikalishe Biochemie, Regensberg, Germany
  
   
  
  Salmonella enteritidis
  CSDB ID 6451 (all data & tools)
• Article ID: 1408
  Curd H, Liu D, Reeves PR "Relationships among the O-antigen gene clusters of Salmonella enterica groups B, D1, D2, and D3" - Journal of Bacteriology 180(4) (1998) 1002-1007
  

  The O antigen is an important cell wall antigen of gram-negative bacteria, and the genes responsible for its biosynthesis are located in a gene cluster. We have cloned and sequenced the DNA segment unique to the O-antigen gene cluster of Salmonella enterica group D3. This segment includes a novel O-antigen polymerase gene (wzyD3). The polymerase gives α(1→6) linkages but has no detectable sequence similarity to that of group D2, which confers the same linkage. We find the remnant of a D3-like wzy gene in the O-antigen gene clusters of groups D1 and B and suggest that this is the original wzy gene of these O-antigen gene clusters.

  gene, O-antigen, O antigen, group, cluster, gene cluster, Salmonella, Salmonella enterica, relationship

  NCBI PubMed ID: 9473060
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: reeves@angis.usyd.edu.au
  Institutions: Department of Microbiology, The University of Sydney,Australia
  
   
  
  Salmonella enterica D1 (O9)
  CSDB ID 6608 (all data & tools)
• 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
  
   
  
  Salmonella enteritidis D1, Salmonella typhi AS D1
  CSDB ID 108609 (all data & tools)
• Article ID: 3244
  Snyder DS, Gibson D, Heiss C, Kay W, Azadi P "Structure of a capsular polysaccharide isolated from Salmonella enteritidis" - Carbohydrate Research 341(14) (2006) 2388-2397
  

  Salmonella enteritidis is a food-borne enteric human pathogen that can form a complex protective extracellular matrix. We describe here a component of this matrix which is distinct from other known salmonella extracellular polysaccharides such as cellulose and colanic acid. We have used glycosyl composition and linkage analysis, as well as 1D and 2D NMR spectroscopy to determine the structure of this polysaccharide. We propose that the primary saccharide in the S. enteritidis capsule has a branched tetrasaccharide repeating unit having the following structure: →3)-α-D-Galp-(1→2)-[α-Tyvp-(1→3)]-α-D-Manp-(1→4)-α-L-Rhap-(1→. This structure is partially substituted on both tyvelose and galactose with a glucose-containing side chain. It further bears considerable similarity to the O antigen from this organism, a feature found in a number of other capsules from Gram-negative bacteria. In addition, we have detected fatty acids at levels that indicate the presence of a lipid anchor.

  Extracellular matrix; Capsule; Salmonella; O Antigen; Capsular polysaccharide; Glycolipid

  Publication DOI: 10.1016/j.carres.2006.06.010
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: azadi@ccrc.uga.edu
  Institutions: Complex Carbohydrate Research Center, Athens, GA 30602-4712, USA, Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
  Methods: NMR, composition analysis, linkage analysis
  
   
  
  Salmonella enteritidis
  CSDB ID 20065 (all data & tools)
• Article ID: 3285
  Nnalue NA, Weintraub A, Oscarson S, Lindberg AA "Cross-reactivity between the mannan of Candida species, Klebsiella K24 polysaccharide and Salmonella C1 and E O-antigens is mediated by a terminal non-reducing b-mannosyl residue" - European Journal of Biochemistry 220(3) (1994) 973-979
  

  Rat monoclonal antibody MASC1-MR9 (MR9) binds to a mannan of Candida species and the O-antigenic polysaccharides of Salmonella bacteria of serogroups C1 (CO) and E (EO). Mannan and glycoconjugates comprising BSA and O-antigen polysaccharides, decasaccharide-BSA (CO-BSA) or trisaccharide-BSA (EO-BSA), inhibited each other's reactivity with MR9. The saccharides β-D-Manp-(1→6)-α-D-Manp-1-OMe, β-D-Manp(1→3)-α-D-Manp-1-OMe, β-D-Manp(1→2)-α-D-Manp-1-OMe (corresponds to the terminal non-reducing end of Salmonella serogroup C1 O-antigen) and β-D-Manp(1→4)-α-L-Rhap(1→3)-α-D-Galp-1-O-p-trifluoroacetamido aniline (corresponds to the backbone of Salmonella serogroup E O-antigen) inhibited the binding of MR9 to these antigens whereas α-D-Manp(1→3)-α-D-Manp-1-OMe and α-D-Manp(1→4)-α-L-Rhap-1-O-p-nitrophenyl did not. Saccharides (3-10 residues) of mammalian origin with terminal and internal Manp α-1→2, Manp α-1→3 and Manp α-1→6 residues also failed to inhibit at any concentration. None of the saccharides with internal β-mannosyl residue was able to inhibit the MR9 antibody. Monosaccharides D-mannose, β-D-Manp-1-OMe and 1,5 anhydro-D-mannitol inhibited the MR9 monoclonal antibody whereas α-D-Manp-1-OMe, β-D-Glcp-1-OMe, and β-D-Galp-1-OMe did not. In addition a Klebsiella K24 capsular polysaccharide containing a β-D-Manp(1→4)-α-D-GlcA (GlcA, glucuronic acid) as a structural element possessed an inhibitory activity. MR9 therefore recognizes an epitope within β-mannose monosaccharide residues at the terminal non-reducing ends of carbohydrate chains in mannan, and polysaccharides in Salmonella serogroups CO and EO and Klebsiella K24.

  O-antigen, epitope, monoclonal antibodies, capsular polysaccharide, serogroup, Salmonella, Klebsiella, cross-reactivity, Candida

  NCBI PubMed ID: 7511532
  Publication DOI: 10.1111/j.1432-1033.1994.tb18701.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Department of Immunology, Microbiology, Pathology and Infectious Diseases, Karolinska Institute, Huddinge University Hospital, Sweden.
  Methods: serological methods
  
   
  
  Salmonella sp. D1
  CSDB ID 22470 (all data & tools)
• Article ID: 3602
  Son S, Tano C, Furuike T, Sakairi N "Synthesis of a tetrasaccharide repeating unit of O-antigenic polysaccharide of Salmonella enteritidis by use of unique and odorless dodecyl thioglycosyl donors" - Tetrahedron Letters 49(36) (2008) 5289-5292
  

  The first total synthesis of a unique tetrasaccharide repeating unit of lipopolysaccharide from Salmonella enteritidis has been accomplished by assembly of dodecyl thioglycosides. The crucial key steps were preparation of a rare branched dideoxy sugar, dtyvelose (3,6-dideoxy-d-arabino-d-hexose) and sequential regioselective glycosylation at 2,3-positions of a central d-mannose residue 5 with d-tyvelose 6 and d-galactose donors 7.

  synthesis, tetrasaccharide, O-antigenic polysaccharide, glycosylation, Salmonella enteritidis

  Publication DOI: 10.1016/j.tetlet.2008.06.097
  Journal NLM ID: 2984819R
  Publisher: Elsevier
  Correspondence: nsaka@ees.hokudai.ac.jp (N. Sakairi)
  Institutions: Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
  Methods: 13C NMR, 1H NMR, NMR-2D, chemical synthesis, glycosylation
  
   
  
  Salmonella enteritidis
  CSDB ID 23432 (all data & tools)
• Article ID: 3747
  Olsson JD, Landstrom J, Ronnols J, Oscarson S, Widmalm G "Synthesis of and molecular dynamics simulations on a tetrasaccharide corresponding to the repeating unit of the capsular polysaccharide from Salmonella enteritidis" - Organic and Biomolecular Chemistry 7(8) (2009) 1612-1618
  

  Syntheses of two oligosaccharides as methyl glycosides related to the repeating unit of S. enteritidis capsular polysaccharide (CPS) are presented. The trisaccharide corresponds to the backbone of the CPS whereas the tetrasaccharide is a model for the repeating unit which has a branched structure. Molecular dynamics simulations investigating their flexibility and dynamics revealed that the oligosaccharides populate several conformational states and indicate that conformational averaging should be used in describing the accessible conformational space.

  synthesis, capsular polysaccharide, conformational, molecular dynamics, Salmonella enteritidis

  NCBI PubMed ID: 19343247
  Publication DOI: 10.1039/b823428k
  Journal NLM ID: 101154995
  Publisher: The Royal Society of Chemistry
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, chemical methods, MD simulations
  
   
  
  Salmonella enteritidis
  CSDB ID 23795 (all data & tools)
• Article ID: 3847
  Gajdus J, Glosnicka R, Szafranek J "Primary structure of Salmonella spp. O-antigens" - Wiadomosci Chemiczne [Polish] 60(9-10) (2006) 621-653
  

  Salmonella spp. are pathogenic Gram-negative bacteria that belong to Enterobacteriaceae family with lipopolysaccharide (LPS) as a constituent of cell wall. This is an integral component of the outer membrane of the wall. Salmonella smooth (S) forms produce LPS, which is composed of three parts, chemically bonded together viz. polysaccharide O-antigen, oligosaccharide core region and lipid A. Antigens O (O-PS) together with H flagella antigens are the foundation of serological classification of these bacteria. O-chain, which is built with up to 50 oligosaccharide repeating units, is one of the products of mild acidic hydrolysis of LPS. Due to the fact that polysaccharide antigens are the sites of specific antibody complexing, any difference in primary and secondary structures of O-antigens reflect serological specificity of bacteria. Taking this fact into consideration, we can distinguish about 2541 Salmonella serotypes with O and H antigenic formulas defined [4]. In this review we present 55 chemical structures of O-antigenic repeating units of Salmonella strains including their heterogeneity structures. The structures can have 22 different monosaccharide residues usually in 3 to 6 sugar repeating units. We describe here selected chemical and spectroscopic (MS, NMR) methods for primary structure examination of these bacterial O-PS. Enzymatic and immunochemical methods are also described. Cross-reactions of Salmonella spp. with any other bacteria or blood group A, B, 0 antigens are explained on the molecular level. Thus, structural assignments of somatic antigens of Salmonella spp. allow us to understand the molecular level of the classification system of these bacteria.

  NMR spectroscopy, O-antigens, Salmonella, MS, primary structure

  WWW link: http://baztech.icm.edu.pl/baztech/cgi-bin/btgetdoc.cgi?BUS2-0016-0014
  Publisher: Polish Chemical Society
  Correspondence: jerzyg@chemik.chem.univ.gda.pl
  Institutions: Wydzial Chemii, Uniwersytet Gdanski, ul. Sobieskiego 18, 80-952 Gdansk
  
   
  
  Salmonella enteritidis D0(O9)
  CSDB ID 25615 (all data & tools)
• Article ID: 4315
  Hong Y, Cunneen MM, Reeves PR "The Wzx translocases for Salmonella enterica O-antigen processing have unexpected serotype specificity" - Molecular Microbiology 84(4) (2012) 620-630
  

  Most Gram-negative bacteria have an O antigen, a polysaccharide with many repeats of a short oligosaccharide that is a part of the lipopolysaccharide, the major lipid in the outer leaflet of the outer membrane. Lipopolysaccharide is variable with 46 forms in Salmonella enterica that underpin the serotyping scheme. Repeat units are assembled on a lipid carrier that is embedded in the cell membrane, and are then translocated by the Wzx translocase from the cytoplasmic face to the outer face of the cell membrane, followed by polymerization. The O antigen is then incorporated into lipopolysaccharide and exported to the outer membrane. The Wzx translocase is widely thought to be specific only for the first sugar of the repeat unit, despite extensive variation in both O antigens and Wzx translocases. However, we found for S. enterica groups B, D2 and E that Wzx translocation exhibits significant specificity for the repeat-unit structure, as variants with single sugar differences are translocated with lower efficiency and little long-chain O antigen is produced. It appears that Wzx translocases are specific for their O antigen for normal levels of translocation.

  O-antigen, Salmonella enterica, wzx

  NCBI PubMed ID: 22497246
  Publication DOI: 10.1111/j.1365-2958.2012.08048.x
  Journal NLM ID: 8712028
  Publisher: Blackwell Publishing
  Correspondence: peter.reeves@sydney.edu.au
  Institutions: School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia
  Methods: SDS-PAGE, genetic methods
  
   
  
  Salmonella enterica D1
  CSDB ID 28394 (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
  
   
  
  Salmonella enterica ssp. enterica sv. Enteritidis I.S. O9 64, Salmonella enterica ssp. enterica sv. Gallinarum bv. Pullorum 11
  CSDB ID 27412 (all data & tools)
• Article ID: 4477
  Andres D, Gohlke U, Broeker NK, Schulze S, Rabsch W, Heinemann U, Barbirz S, Seckler R "An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as non-solution conformers" - Glycobiology 23(4) (2013) 486-494
  

  Bacteriophage P22 recognizes O-antigen polysaccharides of Salmonella enterica subsp. enterica (S.) with its tailspike protein (TSP). In the serovars S. Typhimurium, S. Enteritidis, and S. Paratyphi A, the tetrasaccharide repeat units of the respective O-antigens consist of an identical main chain trisaccharide but different 3,6-dideoxyhexose substituents. Here, the epimers abequose, tyvelose, and paratose determine the specific serotype. P22TSP recognizes O-antigen octasaccharides in an extended binding site with a single 3,6-dideoxyhexose binding pocket. We have isolated S. Paratyphi A octasaccharides which were not available previously and determined the crystal structure of their complex with P22TSP. We discuss our data together with crystal structures of complexes with S. Typhimurium and S. Enteritidis octasaccharides determined earlier. Isothermal titration calorimetry (ITC) showed that S. Paratyphi A octasaccharide binds P22TSP less tightly, with a difference in binding free energy of approximately 7 kJ/mol at 20 degrees C compared to S. Typhimurium and S. Enteritidis octasaccharides. Individual protein-carbohydrate contacts were probed by amino acid replacements showing that the dideoxyhexose pocket contributes to binding of all three serotypes. However, S. Paratyphi A octasaccharides bind in a conformation with an energetically unfavorable varphi / psi glycosidic bond angle combination. By contrast, octasaccharides from the other serotypes bind as solution-like conformers. Two water molecules are conserved in all P22TSP complexes with octasaccharides of different serotypes. They line the dideoxyhexose binding pocket and force the S. Paratyphi A octasaccharides to bind as non-solution conformers. This emphasizes the role of solvent as part of carbohydrate binding sites.

  Salmonella enterica, paratose, bacterial O-antigen, carbohydrate interaction, structural thermodynamics, tailspike protein

  NCBI PubMed ID: 23292517
  Publication DOI: 10.1093/glycob/cws224
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Correspondence: seckler@uni-potsdam.de; barbirz@uni-potsdam.de
  Institutions: Physikalische Biochemie, Universitat Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
  Methods: crystallography, thermodynamics, statistical analysis, crystallization, surface plasmon resonance (SPR), ITC
  
   
  
  Salmonella enterica ssp. enterica sv. Enteritidis
  CSDB ID 29424 (all data & tools)
• Article ID: 4683
  Hong Y, Reeves PR "Diversity of O-antigen repeat unit structures can account for the substantial sequence variation of Wzx translocases" - Journal of Bacteriology 196(9) (2014) 1713-1722
  

  The most common system for synthesis of cell surface polysaccharides is the Wzx/Wzy-dependent pathway, which involves synthesis, on the cytoplasmic face of the cell membrane, of repeat units, which are then translocated to the periplasmic face by a Wzx translocase and then polymerized by Wzy to generate the polysaccharide. One such polysaccharide is O antigen, which is incorporated into lipopolysaccharide (LPS). The O antigen is extremely variable, with over 186 forms in Escherichia coli. Wzx proteins are also very diverse, but they have been thought to be specific only for the first sugar of the repeat units. However, recent studies demonstrated examples in which Wzx translocases have considerable preference for their native repeat unit, showing that specificity can extend well beyond the first sugar. These results appear to be in conflict with the early conclusions, but they involved specificity for side branch residues and could be a special case. Here we take six Wzx translocases that were critical in the earlier studies on the importance of the first sugar and assess their ability to translocate the Escherichia coli O16 and O111 repeat units. We use gene replacements to optimize maintenance of expression level and show that under these conditions the native translocases are the most effective for their native repeat unit, being, respectively, 64-fold and 4-fold more effective than the next best. We conclude that Wzx translocases are commonly adapted to their native repeat unit, which provides an explanation for the great diversity of wzx genes.

  Lipopolysaccharide, structure, polysaccharide, O-antigen, Escherichia coli, specificity, Cell Membrane, membrane, surface polysaccharide, diversity

  Publication DOI: 10.1128/JB.01323-13
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: peter.reeves@sydney.edu.au
  Institutions: School of Molecular Bioscience (G08), University of Sydney, New South Wales, Australia
  Methods: SDS-PAGE, genetic methods, cloning
  
   
  
  Salmonella enterica D1
  CSDB ID 30273 (all data & tools)
• Article ID: 6102
  Liu MA, Kidambi A, Reeves PR "The low level of O antigen in Salmonella enterica Paratyphi A is due to inefficiency of the glycosyltransferase WbaV" - FEMS Microbiology Letters 368(3) (2021) fnab009
  

  The group A O antigen is the major surface polysaccharide of Salmonella enterica serovar Paratyphi A (SPA), and the focal point for most current vaccine development efforts. The SPA O-antigen repeat (O unit) is structurally similar to the group D1 O unit of S. enterica serovar Typhi, differing only in the presence of a terminal side-branch paratose (Par) in place of tyvelose (Tyv), both of which are attached by the glycosyltransferase WbaV. The two O-antigen gene clusters are also highly similar, but with a loss-of-function mutation in the group A tyv gene and the tandem amplification of wbaV in most SPA strains. In this study, we show that SPA strains consistently produce less O antigen than their group D1 counterparts and use an artificial group A strain (D1 Deltatyv) to show this is due to inefficient Par attachment by WbaV. We also demonstrate that group A O-antigen production can be increased by overexpression of the wbaV gene in both the D1 Deltatyv strain and two multi-wbaV SPA strains. These findings should be broadly applicable in ongoing vaccine development pipelines, where efficient isolation and purification of large quantities of O antigen is of critical importance

  biosynthesis, O antigen, glycosyltransferase, paratose, Paratyphi A, WbaV

  NCBI PubMed ID: 33476372
  Publication DOI: 10.1093/femsle/fnab009
  Journal NLM ID: 7705721
  Publisher: Blackwell Publishing
  Correspondence: peter.reeves@sydney.edu.au
  Institutions: School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
  Methods: PCR, SDS-PAGE, genetic methods, extraction, growth assays
  
   
  
  Salmonella enterica D1
  CSDB ID 9691 (all data & tools)
• Article ID: 6383
  Fontana C, Widmalm G "Primary Structure of Glycans by NMR Spectroscopy" - Chemical Reviews 123(3) (2023) 1040-1102
  

  Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.

  NMR, glycan

  NCBI PubMed ID: 36622423
  Publication DOI: 10.1021/acs.chemrev.2c00580
  Journal NLM ID: 2985134R
  Publisher: Chem Rev
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, Departamento de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
  
   
  
  Salmonella enteritidis
  CSDB ID 22383 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136791,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_174035,IEDB_190606,IEDB_225177,IEDB_840979,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_7,SB_72

• Article ID: 1260
  Steinbacher S, Baxa U, Miller S, Weintraub A, Seckler R, Huber R "Crystal structure of phage P22 tailspike protein complexed with Salmonella sp O-antigen receptors" - Proceedings of the National Academy of Sciences of the USA 93(20) (1996) 10584-10588
  

  The O-antigenic repeating units of lipopolysaccharides from Salmonella serogroups A, B, and D1 serve as receptors for the phage P22 tailspike protein, which also has receptor destroying endoglycosidase (endorhamnosidase) activity, integrating the functions of both hemagglutinin and neuraminidase in influenza virus. Crystal structures of the tailspike protein in complex with oligosaccharides, comprising two O-antigenic repeating units from Salmonella typhimurium, Salmonella enteritidis, and Salmonella typhi 253Ty were determined at 1.8 A resolution. The active-site topology with Asp-392, Asp-395, and Glu-359 as catalytic residues was identified. Kinetics of binding and cleavage suggest a role of the receptor destroying endorhamnosidase activity primarily for detachment of newly assembled phages.

  structure, O-antigen, Salmonella, crystal structure, endoglycosidase, hemagglutinin, phage, virus

  NCBI PubMed ID: 8855221
  Journal NLM ID: 7505876
  Publisher: National Academy of Sciences
  Institutions: Abteilung Strukturforschung, Max-Planck-Institut fur Biochemie, Martinsried, Germany, Physikalische Biochemie, Universitat Regensburg, Regensburg, Germany, Department of Immunology, Microbiology, Pathology and Infectious Diseases, Division of Clinical Bacteriology, Huddinge University Hospital, Karolinska Institutet, Huddinge, Sweden
  Methods: X-ray
  
   
  
  Salmonella enterica D1
  CSDB ID 5014 (all data & tools)
• Article ID: 1323
  Zegelaar-Jaarsveld K, van der Plas SC, van der Marel GA, van Boom JH "Preparation of disaccharide haptens corresponding to Salmonella serogroups B and D" - Journal of Carbohydrate Chemistry 15 (1996) 665-689
  

  The properly protected ethyl 1-thio-abequopyranoside 11 and ethyl 1-thio-tyvelopyranoside 26 were prepared by a sequence of reactions, the key steps of which was the regioselective hydride-mediated ring-opening of the cyclic sulfate function in compound 8 and 18. Iodonium ion-assisted glycosylation of allyl mannopyranoside 30 with the individual ethyl 3,6-dideoxy-1-thio-D-hexopyranoside donors 11 and 26 furnished, after deprotection, the respective allyl 3-O-(a-D-abequopyranosyl)-a-D-mannopyranoside 1 and allyl 3-O-(a-D-tyvelopyranosyl)-a-D-mannopyranoside 2.

  synthesis, oligosaccharide, polysaccharide, epitope, serogroup, Salmonella, hapten, disaccharide, abequose, tyvelose

  Publication DOI: 10.1080/07328309608005684
  Journal NLM ID: 8218151
  Publisher: Marcel Dekker
  Institutions: Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, The Netherlands
  
   
  
  Salmonella enterica D (O9)
  CSDB ID 6142 (all data & tools)
• Article ID: 1369
  Baxa U, Steinbacher S, Miller S, Weintraub A, Huber R, Seckler R "Interactions of phage P22 tails with their cellular receptor, Salmonella O-antigen polysaccharide" - Biophysical Journal 71 (1996) 2040-2048
  

  Bacteriophage P22 binds to its cell surface receptor, the repetitive O-antigen structure in Salmonella lipopolysaccharide, by its six homotrimeric tailspikes. Receptor binding by soluble tailspikes and the receptor-inactivating endorhamnosidase activity of the tailspike protein were studied using octa- and dodecasaccharides comprising two and three O-antigen repeats of Salmonella enteritidis and Salmonella typhimurium lipopolysaccharides. Wild-type tailspike protein and three mutants (D392N, D395N, and E359Q) with defective endorhamnosidase activity were used. Oligosaccharide binding to all three subunits, measured by a tryptophan fluorescence quench or by fluorescence depolarization of a coumarin label attached to the reducing end of the dodecasaccharide, occurs independently. At 10 degrees C, the binding affinities of all four proteins to oligosaccharides from both bacterial strains are identical within experimental error, and the binding constants for octa- and dodecasaccharides are 1 x 10(6) M(-1) and 2 x 10(6) M(-1), proving that two O-antigen repeats are sufficient for lipopolysaccharide recognition by the tailspike. Equilibration with the oligosaccharides occurs rapidly, but the endorhamnosidase produces only one cleavage every 100 s at 10 degrees C or about 2 min(-1) at the bacterial growth temperature. Thus, movement of virions in the lipopolysaccharide layer before DNA injection may involve the release and rebinding of individual tailspikes rather than hydrolysis of the O-antigen.

  polysaccharide, O-antigen, O antigen, Salmonella, interaction, cellular, receptor, phage

  NCBI PubMed ID: 8889178
  Journal NLM ID: 0370626
  Publisher: Cambridge, MA: Cell Press
  Correspondence: robert.seckler@biologie.uniregensburg.de
  Institutions: Universitat Regensberg, Phusikalishe Biochemie, Regensberg, Germany
  
   
  
  Salmonella typhi
  CSDB ID 6247 (all data & tools)
• Article ID: 1485
  Steinbacher S, Miller S, Baxa U, Weintraub A, Seckler R "Interaction of Salmonella phage P22 with its O-antigen receptor studied by X-ray crystallography" - Biological Chemistry 378(3-4) (1997) 337-343
  

  The O-antigenic repeating units of the Salmonella cell surface lipopolysaccharides (serotypes A, B and D1) serve as receptors for phage P22. This initial binding step is mediated by the tailspike protein (TSP), which is present in six copies on the base plate of the phage. In addition to the binding activity, TSP also displays a low endoglycolytic activity, cleaving the α(1,3)-O-glycosidic bond between rhamnose and galactose of the O-antigenic repeats. The crystal structure of TSP in complex with receptor fragments allowed to identify the receptor binding site for the octasaccharide product of the enzymatic action of TSP on delipidated LPS and the active site consisting of Asp392, Asp395 and Glu359. The structure comprises a large right-handed parallel beta-helix of 13 turns. These fold independently in the trimer, whereas the N-terminus forms a cap-like structure and the C-terminal parts of the three polypeptide strands merge to a single common domain. In addition, TSP has served as model system for the folding of large, multisubunit proteins. Its folding pathway is influenced by a large number of point mutations, classified as lethal, temperature sensitive or general suppressor mutations, which influence the partitioning between aggregation and the productive folding pathway.

  O-antigen, Salmonella, crystal structure, endoglycosidase, X-ray crystallography, phage mutants, protein folding, receptor binding, β-helix, virus proyein

  NCBI PubMed ID: 9165091
  Journal NLM ID: 9700112
  Publisher: Berlin: Walter De Gruyter
  Institutions: Max-Planck-Institut für Biochemie, Abteilung für Strukturforschung, Martinsried, Germany, Institut für Biophysik und Physikalische Biochemie, Universitat Regensburg, D-93040 Regensburg, Germany, Department of Immunology, Pathology and Infectious Diseases Division of Clinical Bacteriology, Huddinge University Hospital, Karolinska Institutet, Huddinge, Sweden
  Methods: X-ray
  
   
  
  Salmonella sp. D1
  CSDB ID 31415 (all data & tools)
• Article ID: 1674
  Whitfield C, Valvano MA "Biosynthesis and expression of cell-surface polysaccharides in gram-negative bacteria" - Advances in Microbial Physiology 35 (1993) 135-246
  

  This chapter provides an overview of the molecular mechanisms involved in synthesis and expression of cell-surface polysaccharides in Gram-negative bacteria. Biosynthesis of many cell-surface components, including polysaccharides, involves enzymes and enzyme complexes found in the cytoplasmic membrane. The peptidoglycan layer is located immediately external to the cytoplasmic membrane and this layer is required for cell shape and rigidity. Gram-negative bacteria possess a periplasm that contains a variety of proteins and enzymes, including some involved in import and export of macromolecules. Biosynthesis of bacterial cell-surface polysaccharides involves a series of sequential processes: (1) biosynthesis of activated precursors in the cytoplasm, (2) formation of repeating units, (3) polymerization of repeating units, and (d) export of polysaccharides to the cell surface. The assembly of polysaccharide repeating units and subsequent polymerization reactions occur at the cytoplasmic membrane, using precursors synthesized in the cytoplasm. Genes for biosynthesis of cell-surface polysaccharides are chromosomal and are arranged in clusters of one or more transcriptional units. The synthesis of lipopolysaccharide (LPS) may be subject to complex regulation, but on-off switching is not possible due to the essential structural requirement for the lipid A-core LPS molecule. Most bacteria use extracellular polysaccharides (EPSs) for protection, and many regulatory strategies are directed to modulating EPS synthesis in response to appropriate environmental cues. Application of genetic and biochemical approaches has facilitated detailed analysis of complex, multicomponent systems, such as those involved in synthesis of cell-surface polysaccharides.

  NCBI PubMed ID: 8310880
  Publication DOI: 10.1016/S0065-2911(08)60099-5
  Journal NLM ID: 0117147
  Institutions: Department of Microbiology, University of Guelph, Ontario, Canada, Department of Microbiology, University of Guelph, Guelph, Ontario, Canada, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada, N6A 5C1
  
   
  
  Salmonella enterica D1
  CSDB ID 101051 (all data & tools)
• Article ID: 3847
  Gajdus J, Glosnicka R, Szafranek J "Primary structure of Salmonella spp. O-antigens" - Wiadomosci Chemiczne [Polish] 60(9-10) (2006) 621-653
  

  Salmonella spp. are pathogenic Gram-negative bacteria that belong to Enterobacteriaceae family with lipopolysaccharide (LPS) as a constituent of cell wall. This is an integral component of the outer membrane of the wall. Salmonella smooth (S) forms produce LPS, which is composed of three parts, chemically bonded together viz. polysaccharide O-antigen, oligosaccharide core region and lipid A. Antigens O (O-PS) together with H flagella antigens are the foundation of serological classification of these bacteria. O-chain, which is built with up to 50 oligosaccharide repeating units, is one of the products of mild acidic hydrolysis of LPS. Due to the fact that polysaccharide antigens are the sites of specific antibody complexing, any difference in primary and secondary structures of O-antigens reflect serological specificity of bacteria. Taking this fact into consideration, we can distinguish about 2541 Salmonella serotypes with O and H antigenic formulas defined [4]. In this review we present 55 chemical structures of O-antigenic repeating units of Salmonella strains including their heterogeneity structures. The structures can have 22 different monosaccharide residues usually in 3 to 6 sugar repeating units. We describe here selected chemical and spectroscopic (MS, NMR) methods for primary structure examination of these bacterial O-PS. Enzymatic and immunochemical methods are also described. Cross-reactions of Salmonella spp. with any other bacteria or blood group A, B, 0 antigens are explained on the molecular level. Thus, structural assignments of somatic antigens of Salmonella spp. allow us to understand the molecular level of the classification system of these bacteria.

  NMR spectroscopy, O-antigens, Salmonella, MS, primary structure

  WWW link: http://baztech.icm.edu.pl/baztech/cgi-bin/btgetdoc.cgi?BUS2-0016-0014
  Publisher: Polish Chemical Society
  Correspondence: jerzyg@chemik.chem.univ.gda.pl
  Institutions: Wydzial Chemii, Uniwersytet Gdanski, ul. Sobieskiego 18, 80-952 Gdansk
  
   
  
  Salmonella typhi D1 (O9)
  CSDB ID 25614 (all data & tools)
• Article ID: 4759
  Hong Y, Morcilla VA, Liu MA, Russell EL, Reeves PR "Three Wzy polymerases are specific for particular forms of an internal linkage in otherwise identical O units" - Microbiology 163 (2015) 1639-1647
  

  The Wzx/Wzy-dependent pathway is the predominant pathway for O-antigen production in Gram-negative bacteria. The O-antigen repeat unit (O unit) is an oligosaccharide that is assembled at the cytoplasmic face of the membrane on undecaprenyl pyrophosphate. Wzx then flips it to the periplasmic face for polymerisation by Wzy, which adds a O unit to the reducing end of a growing O-unit polymer in each round of polymerisation. Wzx and Wzy both exhibit enormous sequence diversity. We have recently determined that, contrary to earlier reports, the efficiency of diverse Wzx forms can be significantly reduced by minor structural variations to their native O-unit substrate. However, details of Wzy substrate specificity remain unexplored. The closely related galactose-initiated Salmonella O antigens present a rare opportunity to address these matters. The D1 and D2 O units differ only in an internal mannose-rhamnose linkage, and D3 expresses both in the same chain. We showed that D1 and D2 polymerases are specific for O units with their respective alpha or beta configuration for the internal mannose-rhamnose linkage. The Wzy encoded by D3 gene cluster polymerises only D1 O units, and deleting the gene does not eliminate polymeric O antigen, both observations indicating the presence of an additional wzy gene. The levels of Wzx and Wzy substrate specificity will affect the ease with which new O units can evolve, and also our ability to modify O antigens, capsules or secreted polysaccharides by glyco-engineering, to generate novel polysaccharides, as the Wzx/Wzy-dependent pathway is responsible for much of the diversity.

  O-antigen, gene cluster, Salmonella, Substrate Specificity, Wzy polymerases

  NCBI PubMed ID: 25987464
  Publication DOI: 10.1099/mic.0.000113
  Journal NLM ID: 0376646
  Publisher: Washington, DC: Kluwer Academic/Plenum Publishers
  Correspondence: peter.reeves@sydney.edu.au
  Institutions: Department of Microbiology, University of Illinois, Urbana, IL 61801, USA, University of Illinois at Urbana-Champaign, School of Molecular Bioscience, Building D17, University of Sydney, NSW 2006, Australia
  Methods: PCR, SDS-PAGE, DNA techniques, genetic methods
  
   
  
  Salmonella enterica D1
  CSDB ID 30610 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_174035,IEDB_190606,IEDB_225177,IEDB_840979,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_7,SB_72

• Article ID: 1323
  Zegelaar-Jaarsveld K, van der Plas SC, van der Marel GA, van Boom JH "Preparation of disaccharide haptens corresponding to Salmonella serogroups B and D" - Journal of Carbohydrate Chemistry 15 (1996) 665-689
  

  The properly protected ethyl 1-thio-abequopyranoside 11 and ethyl 1-thio-tyvelopyranoside 26 were prepared by a sequence of reactions, the key steps of which was the regioselective hydride-mediated ring-opening of the cyclic sulfate function in compound 8 and 18. Iodonium ion-assisted glycosylation of allyl mannopyranoside 30 with the individual ethyl 3,6-dideoxy-1-thio-D-hexopyranoside donors 11 and 26 furnished, after deprotection, the respective allyl 3-O-(a-D-abequopyranosyl)-a-D-mannopyranoside 1 and allyl 3-O-(a-D-tyvelopyranosyl)-a-D-mannopyranoside 2.

  synthesis, oligosaccharide, polysaccharide, epitope, serogroup, Salmonella, hapten, disaccharide, abequose, tyvelose

  Publication DOI: 10.1080/07328309608005684
  Journal NLM ID: 8218151
  Publisher: Marcel Dekker
  Institutions: Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, The Netherlands
  
   
  
  Salmonella enterica D (O9)
  CSDB ID 6143 (all data & tools)
• Article ID: 1674
  Whitfield C, Valvano MA "Biosynthesis and expression of cell-surface polysaccharides in gram-negative bacteria" - Advances in Microbial Physiology 35 (1993) 135-246
  

  This chapter provides an overview of the molecular mechanisms involved in synthesis and expression of cell-surface polysaccharides in Gram-negative bacteria. Biosynthesis of many cell-surface components, including polysaccharides, involves enzymes and enzyme complexes found in the cytoplasmic membrane. The peptidoglycan layer is located immediately external to the cytoplasmic membrane and this layer is required for cell shape and rigidity. Gram-negative bacteria possess a periplasm that contains a variety of proteins and enzymes, including some involved in import and export of macromolecules. Biosynthesis of bacterial cell-surface polysaccharides involves a series of sequential processes: (1) biosynthesis of activated precursors in the cytoplasm, (2) formation of repeating units, (3) polymerization of repeating units, and (d) export of polysaccharides to the cell surface. The assembly of polysaccharide repeating units and subsequent polymerization reactions occur at the cytoplasmic membrane, using precursors synthesized in the cytoplasm. Genes for biosynthesis of cell-surface polysaccharides are chromosomal and are arranged in clusters of one or more transcriptional units. The synthesis of lipopolysaccharide (LPS) may be subject to complex regulation, but on-off switching is not possible due to the essential structural requirement for the lipid A-core LPS molecule. Most bacteria use extracellular polysaccharides (EPSs) for protection, and many regulatory strategies are directed to modulating EPS synthesis in response to appropriate environmental cues. Application of genetic and biochemical approaches has facilitated detailed analysis of complex, multicomponent systems, such as those involved in synthesis of cell-surface polysaccharides.

  NCBI PubMed ID: 8310880
  Publication DOI: 10.1016/S0065-2911(08)60099-5
  Journal NLM ID: 0117147
  Institutions: Department of Microbiology, University of Guelph, Ontario, Canada, Department of Microbiology, University of Guelph, Guelph, Ontario, Canada, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada, N6A 5C1
  
   
  
  Salmonella enterica D1
  CSDB ID 201051 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 1408
  Curd H, Liu D, Reeves PR "Relationships among the O-antigen gene clusters of Salmonella enterica groups B, D1, D2, and D3" - Journal of Bacteriology 180(4) (1998) 1002-1007
  

  The O antigen is an important cell wall antigen of gram-negative bacteria, and the genes responsible for its biosynthesis are located in a gene cluster. We have cloned and sequenced the DNA segment unique to the O-antigen gene cluster of Salmonella enterica group D3. This segment includes a novel O-antigen polymerase gene (wzyD3). The polymerase gives α(1→6) linkages but has no detectable sequence similarity to that of group D2, which confers the same linkage. We find the remnant of a D3-like wzy gene in the O-antigen gene clusters of groups D1 and B and suggest that this is the original wzy gene of these O-antigen gene clusters.

  gene, O-antigen, O antigen, group, cluster, gene cluster, Salmonella, Salmonella enterica, relationship

  NCBI PubMed ID: 9473060
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: reeves@angis.usyd.edu.au
  Institutions: Department of Microbiology, The University of Sydney,Australia
  
   
  
  Salmonella enterica D3 (O9), Salmonella enterica O27, Salmonella enterica O46, Salmonella enterica D1 (P27) (O9)
  CSDB ID 6611 (all data & tools)
• 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
  
   
  
  Salmonella zuerich D3
  CSDB ID 108612 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136791,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_174035,IEDB_190606,IEDB_225177,IEDB_840979,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_61,SB_67,SB_7,SB_72

• 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
  
   
  
  Salmonella typhi D1
  CSDB ID 108610 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_7,SB_72

• 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
  
   
  
  Salmonella zuerich D3
  CSDB ID 108614 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 1924
  Birnbaum GI, Bundle DR "Conformation of methyl 3,6-dideoxy-a-D-arabino-hexopyranoside, the immunodominant sugar of Salmonella serogroup D1: crystal structure, 1H NMR analysis, and semi-empirical calculations" - Canadian Journal of Chemistry 63(3) (1985) 739-744
  

  Methyl 3,6-dideoxy-α-D-arabino-hexopyranoside (methyl tyveloside) crystallizes in the orthorhombic space group P212121 and the cell dimensions are a = 7.478(1), b = 7.933(1), c = 14.064(1) Å. X-ray intensity data were measured with a diffractometer and the structure was solved by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.038. The pyranose ring exists as an almost perfect 4C1 chair and the conformation adopted by the glycosidic methyl group is in agreement with the requirements of the exo-anomeric effect. Both acetal oxygen atoms act as hydrogen-bond acceptors, and the H...O bond distances are in agreement with this feature. The 1H nmr spectrum shows that the conformation of the pyranose ring in aqueous solution is indistinguishable from that in the crystal. The minimum energy conformation of a pentasaccharide fragment of a Salmonella O-antigen, calculated with tyvelose coordinates obtained by bond modification, is in good agreement with the conformation which was calculated with tyvelose coordinates obtained from the X-ray analysis.

  Publication DOI: 10.1139/v85-122
  Journal NLM ID: 0372705
  Publisher: National Research Council of Canada Canada
  Institutions: Division of'Biologica1 Sciences, National Research Council oj' Canada, Ottawa, Ont., Canada, Division of'Biologica1 Sciences, National Research Council oj' Canada, Ottawa, Ont., Canada KIA OR6
  Methods: 1H NMR, conformation analysis, HSEA
  
   
  
  Salmonella sp. D1
  CSDB ID 112217 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: (->1) 4-nitrophenol
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_174033,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
  CSDB ID 114206 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: LPS
Contained glycoepitopes: IEDB_130660,IEDB_130669,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 2505
  Chernyak AY, Weintraub A, Norberg T, Kallin E "Preparation of oligosaccharide-polyacrylamide conjugates and their use as antigens in enzyme immunoassay (EIA)" - Glycoconjugate Journal 7(2) (1990) 111-119
  

  Oligosaccharides derived from Salmonella lipopolysaccharides or from human milk were converted to their N-acetyl-N-(4-acrylamidophenyl)-1-amino-1-deoxyalditol derivatives. These derivatives were copolymerized with acrylamide to give linear, water-soluble polymers, which were used as coating antigens in EIA assays.

  Lipopolysaccharide, oligosaccharide, Salmonella, conjugate, EIA

  Journal NLM ID: 8603310
  Publisher: Kluwer Academic Publishers
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia, USSR, Department of Clinical Bacteriology, Karolinska Institute, Huddinge University Hospital, Huddinge, Sweden, Organic Synthesis Department, BioCarb AB, Lund, Sweden
  
   
  
  Salmonella enteritidis SH1262
  CSDB ID 128192 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: octasaccharide
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_141798,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 2712
  Jörbeck HJA, Svenson SB, Lindberg AA "Immunochemistry of Salmonella O-antigens: specificity of rabbit antibodies against the O-antigen 4 determinant elicited by whole bacteria and O-antigen 4 specific saccharide-protein conjugates" - Journal of Immunology 123(3) (1979) 1376-1381
  
  NCBI PubMed ID: 89168
  Journal NLM ID: 2985117R
  Publisher: Bethesda, MD: American Association of Immunologists
  
   
  
  Salmonella enteritidis SH1262
  CSDB ID 140013 (all data & tools)
• Article ID: 3501
  Landstrom J, Nordmark EL, Eklund R, Weintraub A, Seckler R, Widmalm G "Interaction of a Salmonella enteritidis O-antigen octasaccharide with the phage P22 tailspike protein by NMR spectroscopy and docking studies" - Glycoconjugate Journal 25(2) (2008) 137-143
  

  The tailspike protein P22 recognizes an octasaccharide derived from the O-antigen polysaccharide of Salmonella enteritidis in a shallow groove and molecular docking successfully identifies this binding region on the protein surface. Analysis by 2D (1)H,(1)H-T-ROESY and transferred NOESY NMR experiments indicate that the bound octasaccharide ligand has a conformation similar to that observed in solution. The results from a saturation transfer difference NMR experiment show that a large number of protons in the octasaccharide are in close contact with the protein as a result of binding. A comparison of the crystal structure of the complex and a molecular dynamics simulation of the octasaccharide with explicit water molecules suggest that only minor conformational changes are needed upon binding to the tailspike protein

  conformation, carbohydrates, molecular dynamics, hydrolase, docking, STD

  NCBI PubMed ID: 17703358
  Journal NLM ID: 8603310
  Publisher: Kluwer Academic Publishers
  Correspondence: gw@organ.su.se
  Institutions: Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, NMR-2D
  
   
  
  Salmonella enteritidis
  CSDB ID 22682 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_141798,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_174035,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_7,SB_72

• Article ID: 2712
  Jörbeck HJA, Svenson SB, Lindberg AA "Immunochemistry of Salmonella O-antigens: specificity of rabbit antibodies against the O-antigen 4 determinant elicited by whole bacteria and O-antigen 4 specific saccharide-protein conjugates" - Journal of Immunology 123(3) (1979) 1376-1381
  
  NCBI PubMed ID: 89168
  Journal NLM ID: 2985117R
  Publisher: Bethesda, MD: American Association of Immunologists
  
   
  
  Salmonella enteritidis SH1262
  CSDB ID 140014 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Aglycon: tetanus toxoid
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136791,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_174035,IEDB_190606,IEDB_225177,IEDB_840979,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_61,SB_67,SB_7,SB_72

• Article ID: 2830
  Saxena M, Di Fabio JL "Salmonella typhi O-polysaccharide-tetanus toxoid conjugated vaccine" - Vaccine 12 (1994) 879-884
  
  Journal NLM ID: 8406899
  Publisher: Elsevier
  
   
  
  Salmonella typhi
  CSDB ID 149612 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit ; n=30
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136791,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_139420,IEDB_139421,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_174035,IEDB_190606,IEDB_225177,IEDB_840979,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_61,SB_67,SB_7,SB_72

• Article ID: 2893
  Hellerqvist CG, Lindberg B, Svensson S, Holme T, Lindberg AA "Structural studies on the O-specific side-chains of the cell-wall lipopolysaccharide from Salmonella typhi and S. enteritidis" - Acta Chemica Scandinavica 23 (1969) 1588-1596
  
  NCBI PubMed ID: 5360616
  Publication DOI: 10.3891/acta.chem.scand.23-1588
  Journal NLM ID: 0421263
  Publisher: Munksgaard International Publishers
  Institutions: Institutionen för organisk kemi, Stockholm Universitet, Stockholm, Sweden, Bakteriologiska Institutionen, Karolinska Institutet, Stockholm, Sweden, Stateus bakteriologiska laboratorium, Stockholm, Sweden
  Methods: NMR, GLC, MS, methylation analysis
  
   
  
  Salmonella enteritidis I.S.64, Salmonella typhi I.S.59
  CSDB ID 100067 (all data & tools)

Show legend Show as text

Structure type: structural motif or average structure
Compound class: LPS
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136044,IEDB_136095,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_1394181,IEDB_1394182,IEDB_139420,IEDB_139421,IEDB_141794,IEDB_141798,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_165,SB_166,SB_187,SB_195,SB_44,SB_67,SB_7,SB_72,SB_88

• Article ID: 3093
  Pappas RS, Sweetman BJ, Ray S, Hellerqvist CG "Monomer sequence determination of carbohydrates using fast-atom bombardment mass spectrometry of periodate-oxidized acetate ester derivatives" - Carbohydrate Research 197 (1990) 1-14
  

  A derivatization method, adapted from that of Angel et al. (ref. 10), for sequencing sugar residues in partially degraded poly- and oligo-saccharides using positive-ion f.a.b.-m.s. is described. Derivative selection provides sequence information by directing fragmentation exclusively to both sides of glycosidic oxygen atoms and, in the case of opened rings, between glycosidic carbon and ring oxygen atoms. Polysaccharides or oligosaccharides are subjected to sequential periodate oxidation, borodeuteride reduction, and acetylation. The derivatized polysaccharides are then subjected to partial degradation, acetylation, and high-performance liquid chromatography (h.p.l.c.) purification. F.a.b.-m.s. data obtained on model compounds, using 3-nitrobenzyl alcohol as matrix for f.a.b.-m.s., demonstrated direction of fragmentation to both sides of the glycosidic oxygen atom in unoxidized residues, and to both sides of the acetal oxygen atoms in oxidized residues. Oligosaccharide linkage and sequence may thus be determined by observing fragmentation from both the reducing and non-reducing ends of the molecule. Two Salmonella lipopolysaccharides, derivatized by this procedure, were partially hydrolyzed and then acetylated. Analysis of the h.p.l.c.-purified oligosaccharide derivatives by f.a.b.-m.s. demonstrated the applicability of the technique for sequencing nmol quantities of branched structures.

  Publication DOI: 10.1016/0008-6215(90)84125-E
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Biochemistry, Vanderbilt University, School of Medicine Nashville, Tennessee 37232, USA
  Methods: FAB-MS, HPLC
  
   
  
  Salmonella strasbourg
  CSDB ID 115841 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_130660,IEDB_130701,IEDB_136105,IEDB_136779,IEDB_136791,IEDB_136906,IEDB_137472,IEDB_139421,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_174033,IEDB_174035,IEDB_190606,IEDB_225177,IEDB_840979,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_7,SB_72

• Article ID: 3226
  Gibson DL, White AP, Snyder SD, Martin S, Heiss C, Azadi P, Surette M, Kay WW "Salmonella Produces an O-Antigen Capsule Regulated by AgfD and Important for Environmental Persistence" - Journal of Bacteriology 188(22) (2006) 7722-7730
  

  In this study, we show that Salmonella produces an O-antigen capsule coregulated with the fimbria- and cellulose-associated extracellular matrix. Structural analysis of purified Salmonella extracellular polysaccharides yielded predominantly a repeating oligosaccharide unit similar to that of Salmonella enterica serovar Enteritidis lipopolysaccharide O antigen with some modifications. Putative carbohydrate transport and regulatory operons important for capsule assembly and translocation, designated yihU-yshA and yihVW, were identified by screening a random transposon library with immune serum generated to the capsule. The absence of capsule was confirmed by generating various isogenic ∆yih mutants, where yihQ and yihO were shown to be important in capsule assembly and translocation. Luciferase-based expression studies showed that AgfD regulates the yih operons in coordination with extracellular matrix genes coding for thin aggregative fimbriae and cellulose. Although the capsule did not appear to be important for multicellular behavior, we demonstrate that it was important for survival during desiccation stress. Since the yih genes are conserved in salmonellae and the O-antigen capsule was important for environmental persistence, the formation of this surface structure may represent a conserved survival strategy.

  gene, O-antigen, extracellular polysaccharide, transposon, Salmonella enterica, capsule, transport, cellulose, regulatory operon

  NCBI PubMed ID: 17079680
  Publication DOI: 10.1128/JB.00809-06
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: wkay@uvic.ca
  Institutions: Department of Biochemistry and Microbiology, University of Victoria, Victoria, V8W 3P6 British Columbia, Canada, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, T2N 4N1 Alberta, Canada, Complex Carbohydrate Research Center, Athens, GA, USA-47123
  Methods: serological methods
  
   
  
  Salmonella enterica sv. Enteritidis
  CSDB ID 20020 (all data & tools)