Found 330 structures.
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1. Compound ID: 83
Structure type: oligomer
Aglycon: p-nitrophenyl
Contained glycoepitopes: IEDB_130648,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_146664,IEDB_190606,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_21,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 17
Blixt O, Van Die I, Norberg T, van den Eijnden DH "High-level expression of the Neisseria meningitidis lgtA gene in Escherichia coli and characterization of the encoded N-acetylglucosaminyltransferase as a useful catalyst in the synthesis of GlcNAcb1→3Gal and GalNAcb1-3Gal linkages" -
Glycobiology 9(10) (1999) 1061-1071
We have expressed the Neisseria meningitidis lgtA gene at a high level in Escherichia coli. The encoded β-N-acetylglucosaminyltransferase, referred to as LgtA, which in the bacterium is involved in the synthesis of the lacto-N-neo-tetraose structural element of the bacterial lipooligosaccharide, was obtained in an enzymatically highly active form. This glycosyltransferase appeared to be unusual in that it displays a broad acceptor specificity toward both α- and β-galactosides, whether structurally related to N- or O-protein-, or lipid-linked oligosaccharides. Product analysis by one- and two-dimensional 400 MHz 1H- and 13C NMR spectroscopy reveals that LgtA catalyzes the introduction of GlcNAc from UDP-GlcNAc in a β1→3-linkage to accepting Gal residues. The enzyme can thus be characterized as a UDP-GlcNAc:Gal α/β-R β 3-N-acetylglucosaminyltransferase. Although lactose is a highly preferred acceptor substrate the recombinant enzyme also acts efficiently on monomeric and dimeric N-acetyllactosamine revealing its potential value in the synthesis of polylactosaminoglycan structures in enzyme assisted procedures. Furthermore, LgtA shows a high donor promiscuity toward UDP-GalNAc, but not toward other UDP-sugars, and can catalyze the introduction of GalNAc in β1→3-linkage to α- or β-Gal in the acceptor structures at moderate rates. LgtA therefore shows promise to be a useful catalyst in the preparative synthesis of both GlcNAc β1→3 Gal and GalNAc β1→3 Gal linkages.
oligosaccharide, enzyme-assisted-synthesis, recombinant glycosyltransferase, glycosidic linkage, polylactosaminoglycan, recombinant glycosyltrasferase
NCBI PubMed ID: 10521543Publication DOI: 10.1093/glycob/9.10.1061Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Institutions: Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden, Department of Medical Chemistry, Vrije Universiteit, Van der Boechorstraat 7, 1081 BT Amsterdam, The Netherlands
Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, enzyme-assisted synthesis, DNA techniques, glycosyltransferase assays, kinetics assays
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2. Compound ID: 179
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a-Neup5Ac-(2-6)-+
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-6)-b-D-Galf-(1-3)-b-D-GalpNAc-(1-3)-b-D-Galp-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_136044,IEDB_136095,IEDB_136794,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_146100,IEDB_149174,IEDB_158551,IEDB_190606,SB_126,SB_165,SB_166,SB_170,SB_171,SB_172,SB_187,SB_195,SB_21,SB_7,SB_84,SB_88
The structure is contained in the following publication(s):
- Article ID: 37
Caroff M, Karibian D "Structure of bacterial lipopolysaccharides" -
Carbohydrate Research 338(23) (2003) 2431-2447
Bacterial lipopolysaccharides are the major components of the outer surface of Gram-negative bacteria They are often of interest in medicine for their immunomodulatory properties. In small amounts they can be beneficial, but in larger amounts they may cause endotoxic shock. Although they share a common architecture, their structural details exert a strong influence on their activity. These molecules comprise: a lipid moiety, called lipid A, which is considered to be the endotoxic component, a glycosidic part consisting of a core of approximately 10 monosaccharides and, in 'smooth-type' lipopolysaccharides, a third region, named O-chain, consisting of repetitive subunits of one to eight monosaccharides responsible for much of the immunospecificity of the bacterial cell.
Lipopolysaccharide, structure, core, lipid A, endotoxin, O-chains
NCBI PubMed ID: 14670707Publication DOI: 10.1016/j.carres.2003.07.010Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: martine.carloff@bbmpc.u-psud.fr
Institutions: Equipe Endotoxines, UMR 8619 du Centre National de la Recherche Scientifique, IBBMC, Université de Paris-Sud, F-Orsay, France
- Article ID: 61
Eserstam R, Rajaguru TP, Jansson PE, Weintraub A, Albert MJ "The structure of the O-chain of the lipopolysaccharide of a prototypal diarrheagenic strain of Hafnia alvei that has characteristics of a new species under the genus Escherichia" -
European Journal of Biochemistry 269(13) (2002) 3289-3295
The structure of the O-polysaccharide of the lipopolysaccharide from a diarrheal strain isolated in Bangladesh was studied with sugar, and methylation analysis, NMR spectroscopy, mass spectrometry and partial acid hydrolysis. The strain was first designated as Hafnia alvei, but later found to be a possible new species in the genus Escherichia. Two different polysaccharides were detected, a major and a minor one. The structure of the major polysaccharide is given below, while the structure of the minor one was not investigated. The structure of the repeating unit was established as The structure does not resemble any of the previously investigated lipopolysaccharide O-chains from Escherichia coli or H. alvei, but could fit in either group based on types of sugar residues and acidity. Phenotypic microbiological studies cannot definitely assign it to either species of the two genera. Genetic hybridization studies indicate that the Bangladeshi isolates may require a new species designation under the genus Escherichia
Lipopolysaccharide, Escherichia coli, Hafnia alvei, diarrhea, neuraminic acid
NCBI PubMed ID: 12084070Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: pererik.jansson@kfcmail.hs.sll.se
Institutions: Clinical Research Center, Analytical Unit, Karolinska Institute, Huddinge Hospital, S-141 86 Huddinge, Sweden
Methods: methylation, NMR-2D, NMR, sugar analysis
- Article ID: 3821
Banoub JH, El Aneed A, Cohen AM, Joly N "Structural investigation of bacterial lipopolysaccharides by mass spectrometry and tandem mass spectrometry" -
Mass Spectrometry Reviews 29(4) (2010) 606-650
Mass spectrometric studies are now playing a leading role in the elucidation of lipopolysaccharide (LPS) structures through the characterization of antigenic polysaccharides, core oligosaccharides and lipid A components including LPS genetic modifications. The conventional MS and MS/MS analyses together with CID fragmentation provide additional structural information complementary to the previous analytical experiments, and thus contribute to an integrated strategy for the simultaneous characterization and correct sequencing of the carbohydrate moiety.
LPS, O-antigen, lipid A, core oligosaccharide, MS and MS/MS analyses
NCBI PubMed ID: 20589944Publication DOI: 10.1002/mas.20258Journal NLM ID: 8219702Publisher: Wiley
Correspondence: joe.banoub@dfo-mpo.gc.ca
Institutions: Fisheries and Oceans Canada, Science Branch, Special Projects, P.O. Box 5667, St. John's, Newfoundland, Canada A1C 5X1, Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada A1B 3V6, College of Pharmacy and Nutrition, University of Saskatchewan, Thorvaldson Building, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9, Unité de Catalyse et de Chimie du Solide, Site de l'Artois—UMR CNRS 8181, I.U.T. de Béthune, Département Chimie, 1230 rue de l'Université, BP819, 62408 Béthune Cedex, France, Institute for Marine Biosciences Room 219A, (NRC-IMB), National Research Council of Canada, Government of Canada, 1411 Oxford Street, Halifax, NS, Canada B3H 3Z1
Methods: MS/MS, MS
- 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_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 5027
Naumenko OI, Zheng H, Senchenkova SN, Wang H, Li Q, Shashkov AS, Wang J, Knirel YA, Xiong Y "Structures and gene clusters of the O-antigens of Escherichia albertii O3, O4, O6, and O7" -
Carbohydrate Research 449 (2017) 17-22
The O-specific polysaccharides (OPSs) called O-antigens were obtained by mild acid degradation of the lipopolysaccharides of Escherichia albertii serotypes O3, O4, O6, and O7 and studied by sugar analysis along with 1D and 2D 1H and 13C NMR spectroscopy. The following structure was established for the OPS of E. albertii O4, which, to our knowledge, is unique among known bacterial polysaccharide structures: -2)-α-l-Rhap-(1-2)-α-l-Fucp-(1-2)-β-d-Galp-(1-3)-α-d-GalpNAc-(1-3)-β-d-GlcpNAc-(1- The OPS structure of the strain of E. albertii O7 studied was identical to that of strain LMG 20973 (= Albert 10457), whose structure has been reported earlier (R. Eserstam et al. Eur. J. Biochem. 269 (2002) 3289-3295). E. albertii O3 and O6 shared the OPS structures with Escherichia coli O181 and O3, respectively, except for the lack of O-acetylation in E. albertii O3, which is present in E. coli O181. The gene clusters driving the O-antigen biosynthesis of the E. albertii strains were sequenced, the genes were annotated by comparison with sequences in the available databases, and the predicted functions of the encoded proteins were found to be consistent with the OPS structures established. In accordance with the relatedness of the OPS structures, the O-antigen gene clusters of E. albertii O3 and O6 contain the same genes and have the same organization as those of E. coli O181 and O3, the entire gene clusters being 83% and 98% identical, respectively.
Lipopolysaccharide, O-antigen, Pseudomonas aeruginosa, Escherichia coli, bacterial polysaccharide structure, O-antigen gene cluster, Enterobacter cloacae, Escherichia albertii
NCBI PubMed ID: 28672166Publication DOI: 10.1016/j.carres.2017.06.008Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: xiongyanwen@icdc.cn
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Zigong Center for Disease Control and Prevention, Zigong, Sichuan Province, China, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, GLC, GPC, acetylation, bioinformatic analysis, sequencing
- Article ID: 5191
Naumenko OI, Zheng H, Xiong Y, Senchenkova SN, Wang H, Shashkov AS, Chizhov AO, Li Q, Knirel YA, Wang J "Structure elucidation of the O-specific polysaccharide by NMR spectroscopy and selective cleavage and genetic characterization of the O-antigen of Escherichia albertii O5" -
Carbohydrate Research 457 (2018) 25-31
The O-specific polysaccharide (O-antigen) was obtained by mild acid degradation of the lipopolysaccharide of Escherichia albertii O5 (strain T150248) and studied by sugar analysis, selective cleavages of glycosidic linkages, and 1D and 2D 1H and 13C NMR spectroscopy. Partial solvolysis with anh (anhydrous) CF3CO2H and hydrolysis with 0.05 M CF3CO2H cleaved predominantly the glycosidic linkage of β-GalpNAc or β-Galf, respectively, whereas the linkages of α-GlcpNAc and β-Galp were stable. Mixtures of the corresponding tri- and tetra-saccharides thus obtained were studied by NMR spectroscopy and high-resolution ESI MS. The following new structure was established for the tetrasaccharide repeat (O-unit) of the O-polysaccharide: →4)-α-d-GlcpNAc-(1→4)-β-d-Galp6Ac-(1→6)-β-d-Galf-(1→3)-β-d-GalpNAc-(1→ where the degree of O-acetylation of d-Galp is ∼70%. The O-polysaccharide studied has a β-d-Galp-(1→6)-β-d-Galf-(1→3)-β-d-GalpNAc trisaccharide fragment in common with the O-polysaccharides of E. albertii O7, Escherichia coli O124 and O164, and Shigella dysenteriae type 3 studied earlier. The orf5-7 in the O-antigen gene cluster of E. albertii O5 are 47%, 78%, and 75% identical on the amino acid level to genes for predicted enzymes of E. albertii O7, including Galp-transferase wfeS, UDP-d-Galp mutase glf, and Galf-transferase wfeT, respectively, which are putatively involved with the synthesis of the shared trisaccharide fragment of the O-polysaccharides. The occurrence upstream of the O-antigen gene cluster of a 4-epimerase gene gnu for conversion of undecaprenyl diphosphate-linked d-GlcNAc (UndPP-d-GlcNAc) into UndPP-d-GalNAc indicates that d-GalNAc is the first monosaccharide of the O-unit, and hence the O-units are interlinked in the O-polysaccharide of E. albertii O5 by the β-d-GalpNAc-(1→4)-α-d-GlcpNAc linkage.
Lipopolysaccharide, Escherichia coli, capsular polysaccharide, O-specific polysaccharide, bacterial polysaccharide structure, selective cleavage, O antigen gene cluster, Escherichia albertii
NCBI PubMed ID: 29309918Publication DOI: 10.1016/j.carres.2017.12.010Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: H. Zheng
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Zigong Center for Disease Control and Prevention, Zigong, Sichuan Province, China, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
Methods: 13C NMR, 1H NMR, NMR-2D, partial acid hydrolysis, sugar analysis, ESI-MS, GLC, mild acid hydrolysis, de-O-acetylation, GPC, bioinformatic analysis, delipidation, partial solvolysis with trifluoroacetic acid
- Article ID: 5481
Naumenko OI, Senchenkova SN, Knirel YA "O-Specific polysaccharides of a new species of enteric bacteria Escherichia albertii closely related to E. coli" -
Russian Journal of Bioorganic Chemistry 45(6) (2019) 451-462
The data on the structure of O-specific polysaccharides (O-antigens) of all nine known molecular types (potential O-serotypes) of a new type of enterobacteria Escherichia albertii, causative agents of intestinal infections in humans and birds, are presented. The advantages and limitations of structural analysis methods used to determine the structure of E. albertii polysaccharides are discussed. The annotation of genes in gene clusters of biosynthesis of O-antigens of E. albertii was carried out by comparison with the sequences in the available databases. Structural and genetic relationships between O-antigens of E. albertii and closely related species of E. coli are discussed. It was found that, in addition to the O-antigen, E. albertii O9 expresses a mannan of the same structure as the mannan of E. coli O8.
biosynthesis, structure, O-antigen, Escherichia coli, O-specific polysaccharide, glycosyltransferase, O-antigen gene cluster, selective cleavage, glycosidic bond, Escherichia albertii, bacterial mannan
Publication DOI: 10.1134/S1068162019060293Journal NLM ID: 9420101Publisher: Springer Science and Business Media
Correspondence: YA Knirel
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: solvolysis with trifluoroacetic acid, acid hydrolysis with CF3CO2H
- Article ID: 5742
Caroff M, Novikov A "Lipopolysaccharides: structure, function and bacterial identification" -
OCL - Oilseeds and fats, Crops and Lipids 27 (2020) 31
Lipopolysaccharides (LPS) are the main components of the outer membrane of Gram-negative bacteria. They are glycolipids containing a lipid moiety called lipid A, more often made of a bis-phosphorylated glucosamine disaccharide, carrying fatty acids in ester and amide linkages. Lipid A is linked to a core oligosaccharide of about 10 sugars, substituted in the wild-type strains, by long-chain oligosaccharide repetitive units, extending outside the bacteria and representing their main antigens. In addition to determine the serotype of the bacterium, LPS are highly potent biological molecules, capable of eliciting at the level of minute amounts, beneficial, as well as deleterious activities.
Lipopolysaccharide, serology, endotoxins, inflammation, structure-activity
Publication DOI: 10.1051/ocl/2020025Publisher: France: EDP Sciences (ISSN: 22726977, 22576614)
Correspondence: martine.caroff@lpsbiosciences.com
Institutions: LPS-BioSciences, Paris-Saclay University, Orsay, France, Hephaistos-Pharma, Paris-Saclay University, Orsay, France
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3. Compound ID: 234
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a-D-GlcpNAc-(1-2)-+
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b-D-Galp-(1-4)-a-D-Glcp-(1-3)-D-gro-a-D-Hepp-(1-3)-+ a-Kdop-(2-4)-+
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b-GalpNAc-(1-3)-b-D-Galp-(1-4)-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Glcp-(1-4)-L-gro-a-D-manHepp-(1-5)-a-Kdop |
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Structure type: oligomer
Compound class: LPS
Contained glycoepitopes: IEDB_130646,IEDB_130648,IEDB_130650,IEDB_130659,IEDB_130697,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_137776,IEDB_1391966,IEDB_140087,IEDB_140108,IEDB_140110,IEDB_140122,IEDB_141794,IEDB_141807,IEDB_142351,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_149144,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_983931,SB_145,SB_165,SB_166,SB_173,SB_187,SB_192,SB_195,SB_21,SB_30,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 59
Erwin AL, Haynes PA, Rice PA, Gotschlich EC "Conservation of the lipooligosaccharide synthesis locus lgt among strains of Neisseria gonorrhoeae: Requirement for lgtE in synthesis of the 2C7 epitope and of the b chain of strain 15253" -
Journal of Experimental Medicine 184 (1996) 1233-1241
The present study was undertaken to examine the extent to which the lgt locus varies among strains of gonococci. This locus encodes five glycosyl transferases involved in the synthesis of the lipooligosaccharide (LOS) of Neisseria gonorrhoeae. We examined seven gonococcal strains and found that the structure of the lgt locus is conserved among six of these strains. The locus is strikingly altered in strain 15253. This is one of the few strains where extensive structural analysis of its LOS is available, and therefore, we defined the altered lgt locus and focused on the reactivity of mAB 2C7. We found that strain 15253 contains only two lgt genes, lgtA and lgtE. As in F62, lgtA encodes a GlcNAc transferase and is subject to phase variation. In addition, by analysis of deletion mutants, we found that lgtE, which encodes a galactosyl transferase that is required for elongating the alpha-chain, is also necessary for completing the beta chain
biosynthesis, synthesis, Lipooligosaccharide, genetics, LOS, Neisseria, strain, chain, locus, epitope, conservation, Gonorrhoeae, lgt, Neisseria gonorrhoeae, requirement
NCBI PubMed ID: 8879194Publication DOI: 10.1084/jem.184.4.1233Journal NLM ID: 2985109RPublisher: Rockefeller University Press
Institutions: Laboratory of Bacterial Pathogenesis and Immunology, Rockefeller University, New York, NY, USA
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4. Compound ID: 552
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b-D-GalpNAc-(1-3)-+
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-6)-b-D-Glcp-(1-3)-b-D-GalpNAc-(1-4)-a-D-Galp-(1- |
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Structure type: polymer chemical repeating unit
Trivial name: O-deacetylated and dephosphorylated polysaccharide (DPS)
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_140529,IEDB_141794,IEDB_142488,IEDB_146664,IEDB_151528,IEDB_167069,IEDB_190606,IEDB_983931,SB_192,SB_21,SB_25,SB_7
The structure is contained in the following publication(s):
- Article ID: 114
Toukach FV, Shashkov AS "Computer-assisted structural analysis of regular glycopolymers on the basis of 13C NMR data" -
Carbohydrate Research 335(2) (2001) 101-104
A computer-assisted approach to the prediction of the primary structures of regular glycopolymers is described. The analysis is based on comparing the calculated 13C NMR spectra of all the possible structures of the repeating unit (for the given monomeric composition) to an experimental 13C NMR spectrum. The spectra generation is based on the spectral database containing information on the 13C chemical shifts of monomers, di- and trimeric fragments. If the required data are missing from this database, the special database for average glycosylation effects is used. The analysis reveals those structures with the calculated 13C NMR spectrum most close to observed. The structures of repeating units of any topology containing up to six residues linked by glycosidic, amidic or phospho-diester bridges can be predicted. Unambiguous selection of the proper structure from the output list of possible structures may require additional experimental data. Testing the created program and databases on bacterial polysaccharides and their derivatives containing up to three non-sugar residues (alditols, amino acids, phosphate groups etc.) per repeating unit revealed the good convergence of prediction with independently obtained structural data.
NMR, structural, analysis, structural analysis, 13C NMR, calculation, computer, glycopolymer, regular
NCBI PubMed ID: 11567641Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: tou@cacr.ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 117913 Moscow, Russian Federation.
Methods: NMR simulation
- Article ID: 494
Torzewska A, Kocharova NA, Maszewska A, Knirel YA, Rozalski A "Serological characterization of the O-specific polysaccharide of Providencia alcalifaciens O23" -
Archivum Immunologiae et Therapiae Experimentalis 52(1) (2004) 43-49
INTRODUCTION: The genus Providencia belongs to the Enterobacteriaceae family and currently consists of five species: P. alcalifaciens, P. heimbachae, P. rettgerii, P. rustigianii and P. stuartii. The serological classification scheme of P. alcalifaciens, P. rustigianii and P. stuartii includes 63 O-serogroups and 30 H-serogroups. The O-antigenic specificity is defined by the structure of the O-antigen (O-specific polysaccharide--OPS), a part of the lipopolysaccharide (LPS, endotoxin), one of the major components of the outer membrane of gram-negative bacteria and an important virulence factor of these bacteria. Among the bacteria of the Enterobacteriaceae family, the genus Providencia is one of the least studied in respect to its LPS structure and antigenic specificity. Studies of the chemical structures and the serological specificity of the O-antigens aim at the elucidation of the molecular basis of the serological classification of Providencia sp. MATERIALS AND METHODS: LPS and alkali-treated LPS of P. alcalifaciens O23 and serologically related P. rustigianii O14, P. mirabilis O13 and P. myxofaciens as well as O-antiserum against P. alcalifaciens O23 were used. Serological characterization of P. alcalifaciens O23 O-specific polysaccharide was done by use enzyme immunosorbent assay (EIA), passive hemolysis test (PHT) as well as by inhibition and sodium deoxycholate polyacrylamide gel electrophoresis (DOC-PAGE) of LPS and Western blot. RESULTS AND CONCLUSIONS: The OPS of P. alcalifaciens, O23, contains an N-(D-glucuronoyl)-N-[(R)-1-carboxyethyl]-L-lysine residue (GlcAAlaLys). The LPS of P. alcalifaciens, O23, and other LPSs containing AlaLys from Providencia and Proteus strains were tested with rabbit anti-P. alcalifiaciens O23 serum. The serological data showed that a GlcAAlaLys-associated epitope plays a role as an antigenic determinant in the P. alcalifaciens O23 OPS and revealed the particular importance of glucuronic acid and the carboxyethyl group for the binding of O23-specific antibodies.
Lipopolysaccharide, structure, characterization, polysaccharide, O-antigen, O-specific, O-specific polysaccharide, Providencia, Providencia alcalifaciens, serological, O-serogroups, Ne-[(R)-1-carboxyethyl]-L-lysine
NCBI PubMed ID: 15053232Journal NLM ID: 0114365Publisher: Basel, Boston: Birkhaüser
Correspondence: rozala@biol.uni.lodz.pl
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Microbiology and Immunology, University of Lodz, Lodz, Poland
- Article ID: 890
Kondakova AN, Toukach FV, Senchenkova SN, Arbatsky NP, Shashkov AS, Knirel YA, Zych K, Torzewska A, Kolodziejska K, Rozalski A, Sidorczyk Z "New structures of the O-specific polysaccharides of Proteus. Part 2. O-Acetylated polysaccharides" -
Biochemistry (Moscow) 67(2) (2002) 201-211
Structures of five new O-specific polysaccharides of Proteus bacteria were established. Four of them, Proteus penneri 4 (O72), Proteus vulgaris 63/57 (O37), Proteus mirabilis TG 277 (O69), and Proteus penneri 20 (O17), contain O-acetyl groups in non-stoichiometric quantities, and the polysaccharide of P. penneri 1 is structurally related to that of P. penneri 4. The structures were elucidated using NMR spectroscopy, including one dimensional 1H- and 13C-NMR spectroscopy, two-dimensional 1H, 1H correlation (COSY, TOCSY), H-detected 1H, 13C heteronuclear multiple-quantum coherence (HMQC), heteronuclear multiple-bond correlation (HMBC), and nuclear Overhauser effect spectroscopy (NOESY or ROESY), along with chemical methods. The structural data obtained are useful as the chemical basis for the creation of the classification scheme for Proteus strains.
structure, Bacterial, polysaccharide, O-antigen, O-specific, O-specific polysaccharide, Proteus, polysaccharides, O-specific polysaccharides, O-acetyl
Publication DOI: 10.1023/A:1014414030784Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Correspondence: knirel@ioc.ac.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: NMR, de-O-acetylation
- Article ID: 1238
Sidorczyk Z, Toukach FV, Zych K, Drzewiecka D, Arbatsky NP, Shashkov AS, Knirel YA "Structural and serological relatedness of the O-antigens of Proteus penneri 1 and 4 from a novel Proteus serogroup O72" -
European Journal of Biochemistry 269(1) (2002) 358-363
O-specific polysaccharides (O-antigens) of the lipopolysaccharides (LPS) of Proteus penneri strains 1 and 4 were studied using sugar analysis, (1)H and (13)C NMR spectroscopy, including 2D COSY, H-detected (1)H,(13)C HMQC, and rotating-frame NOE spectroscopy (ROESY). The following structures of the tetrasaccharide (strain 1) and pentasaccharide (strain 4) repeating units of the polysaccharides were established: [reaction: see text]. In the polysaccharide of P. penneri strain 4, glycosylation with the lateral Glc residue (75%) and O-acetylation of the lateral GalNAc residue (55%) are nonstoichiometric. This polysaccharide contains also other, minor O-acetyl groups, whose positions were not determined. The structural similarity of the O-specific polysaccharides was consistent with the close serological relatedness of the LPS, which was demonstrated by immunochemical studies with O-antisera against P. penneri 1 and 4. Based on these data, it was proposed to classify P. penneri strains 1 and 4 into a new Proteus serogroup, O72, as two subgroups, O72a and O72a,b, respectively. Serological cross-reactivity of P. penneri 1 O-antiserum with the LPS of P. penneri 40 and 41 was substantiated by the presence of an epitope(s) on the LPS core region shared by all P. penneri strains studied.
Lipopolysaccharide, O-antigen, O-specific polysaccharide, Proteus penneri, O-serogroup
NCBI PubMed ID: 11784330Publication DOI: 10.1046/j.0014-2956.2001.02660.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: zsidor@biol.uni.lodz.pl
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of General Microbiology, Institute of Microbiology and Immunology, University of Łodź, Łodź, Poland
Methods: NMR
- Article ID: 3357
Perepelov AV, Liu B, Senchenkova SN, Shevelev SD, Wang W, Shashkov AS, Feng L, Wang L, Knirel YA "The structure of the glycerol phosphate-containing O-specific polysaccharide from Escherichia coli O130" -
Russian Journal of Bioorganic Chemistry 33(1) (2007) 64-68
A phosphorylated O-specific polysaccharide was obtained by mild acidic degradation of the lipopolysaccharide from the enteric bacterium Escherichia coli O130 and characterized by the methods of chemical analysis, including dephosphorylation and 1H and 13C NMR spectroscopy. The polysaccharide was shown to be composed of branched tetrasaccharide repeating units containing two N-acetyl-D-galactosamine residues,D-galactose, D-glucose,and glycerophosphate residues (one of each). The polysaccharide has the following structure, which is unique among the known bacterial polysaccharides:
Escherichia coli, O-specific polysaccharide, teichoic acid, glycerophosphate, structure; NMR spectroscopy
Publication DOI: 10.1134/S1068162007010062Journal NLM ID: 9420101Publisher: Springer Science and Business Media
Correspondence: knirel@ioc.ac.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia,TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, China Tyan-jin Key Laboratory for Microbial Functional Genomics, TEDA College, Nankai University, TEDA, Tyan-jin, China
Methods: 13C NMR, 1H NMR, NMR-2D, HF solvolysis, sugar analysis, 31P NMR, GLC, mild acid hydrolysis, NMR-1D
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5. Compound ID: 555
|
R-CetEtN-(1--P--6)--+
|
-4)-b-D-GalpNAc-(1-3)-a-D-Galp-(1-3)-b-D-GalpNAc-(1-4)-a-D-Galp-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_144988,IEDB_144989,IEDB_144990,IEDB_151528,IEDB_167071,IEDB_190606,SB_21,SB_25,SB_7
The structure is contained in the following publication(s):
- Article ID: 114
Toukach FV, Shashkov AS "Computer-assisted structural analysis of regular glycopolymers on the basis of 13C NMR data" -
Carbohydrate Research 335(2) (2001) 101-104
A computer-assisted approach to the prediction of the primary structures of regular glycopolymers is described. The analysis is based on comparing the calculated 13C NMR spectra of all the possible structures of the repeating unit (for the given monomeric composition) to an experimental 13C NMR spectrum. The spectra generation is based on the spectral database containing information on the 13C chemical shifts of monomers, di- and trimeric fragments. If the required data are missing from this database, the special database for average glycosylation effects is used. The analysis reveals those structures with the calculated 13C NMR spectrum most close to observed. The structures of repeating units of any topology containing up to six residues linked by glycosidic, amidic or phospho-diester bridges can be predicted. Unambiguous selection of the proper structure from the output list of possible structures may require additional experimental data. Testing the created program and databases on bacterial polysaccharides and their derivatives containing up to three non-sugar residues (alditols, amino acids, phosphate groups etc.) per repeating unit revealed the good convergence of prediction with independently obtained structural data.
NMR, structural, analysis, structural analysis, 13C NMR, calculation, computer, glycopolymer, regular
NCBI PubMed ID: 11567641Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: tou@cacr.ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 117913 Moscow, Russian Federation.
Methods: NMR simulation
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6. Compound ID: 729
|
R-3HOBut-(1-3)-b-D-Fucp3N-(1-3)-a-D-GalpNAc-(1-3)-b-D-GalpNAc-(1-3)-+
|
-3)-b-D-GalpNAc-(1-4)-a-D-Galp-(1-6)-b-D-Galp-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS, O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_134624,IEDB_134627,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_147450,IEDB_151528,IEDB_153207,IEDB_153208,IEDB_190606,IEDB_742248,IEDB_885822,SB_163,SB_165,SB_166,SB_187,SB_195,SB_21,SB_23,SB_24,SB_25,SB_7,SB_8,SB_88
The structure is contained in the following publication(s):
- Article ID: 194
Vinogradov EV, Pantophlet R, Dijkshoorn L, Brade L, Holst O, Brade H "Structural and serological characterisation of two O-specific polysaccharides of Acinetobacter" -
European Journal of Biochemistry 239 (1996) 602-610
Extraction of dry bacteria of Acinetobacter strain 34 (DNA group 2) or Acinetobacter strain 108 (DNA group 13) by phenol/water yielded a polymer that was identified by means of serological studies and fatty acid analysis as S-form lipopolysaccharide. Degradation of the lipopolysaccharides of strains 34 and 108 in 1% acetic acid and 5% acetic acid, respectively, and gel-permeation chromatography gave the respective O-antigenic polysaccharides, the structures of which were determined, by compositional analysis and NMR spectroscopy of the polysaccharide, as [Sequence: see text] for strain 108, where D-Fucp3NBuOH represents 3-[(R)-3-hydroxybutyramido] -3,6-dideoxy-D-galactose and D-GalpANAc represents 2-acetamido-2-deoxy-D-galacturonic acid. Both structures were specifically recognised in Western blots by polyclonal rabbit antisera and there was no cross-reaction between these two structures.
Lipopolysaccharide, NMR, Acinetobacter, serology, Western blot
NCBI PubMed ID: 8774703Publication DOI: 10.1111/j.1432-1033.1995.899_3.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: Division of Biochemical Microbiology, Center for Medicine and Biosciences, Research Center Borstel, Germany, Department of Medical Microbiology, Leiden University Hospital, Leiden, The Netherlands
Methods: NMR-2D, NMR, composition analysis
- Article ID: 681
Haseley SR, Wilkinson SG "Structural studies of the putative O-specific polysaccharide of Acinetobacter baumannii O2 containing 3,6-dideoxy-3-N-(D-3-hydroxybutyryl)amino-D-galactose" -
European Journal of Biochemistry 233 (1995) 899-906
A polysaccharide containing D-galactose, 2-deoxy-2-N-acetylamino-D-galactose and 3,6-dideoxy-3-N-(D-3-hydroxybutyryl)amino-D-galactose, probably corresponding to the lipopolysaccharide side chain, was obtained from an aqueous phenol extract of isolated cell walls from Acinetobacter baumannii strain O2. By means of NMR studies and chemical degradations, the repeating unit of the polymer was identified as a branched hexasaccharide of the structure shown, where Fuc3N represents 3-amino-3,6-dideoxygalactose and R represents D-3-hydroxybutyryl. Serological tests indicated that the polymer corresponded to the O2 antigen.
Lipopolysaccharide, Acinetobacter, Acinetobacter baumannii, O-specific polysaccharide, 6-dideoxy-D-galactose, 3-amino-3, 3-hydroxybutyric acid
NCBI PubMed ID: 8521857Publication DOI: 10.1111/j.1432-1033.1995.899_3.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: School of Chemistry, University of Hull, England.
Methods: methylation, NMR-2D, partial acid hydrolysis, NMR, Smith degradation
- 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_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 4534
Hu D, Liu B, Dijkshoorn L, Wang L, Reeves PR "Diversity in the major polysaccharide antigen of Acinetobacter baumannii assessed by DNA sequencing, and development of a molecular serotyping scheme" -
PLoS One 8(7) (2013) e70329
We have sequenced the gene clusters for type strains of the Acinetobacter baumannii serotyping scheme developed in the 1990s, and used the sequences to better understand diversity in surface polysaccharides of the genus. We obtained genome sequences for 27 available serovar type strains, and identified 25 polysaccharide gene cluster sequences. There are structures for 12 of these polysaccharides, and in general the genes present are appropriate to the structure where known. This greatly facilitates interpretation. We also find 53 different glycosyltransferase genes, and for 7 strains can provisionally allocate specific genes to all linkages. We identified primers that will distinguish the 25 sequence forms by PCR or microarray, or alternatively the genes can be used to determine serotype by 'molecular serology'. We applied the latter to 190 Acinetobacter genome-derived gene-clusters, and found 76 that have one of the 25 gene-cluster forms. We also found novel gene clusters and added 52 new gene-cluster sequence forms with different wzy genes and different gene contents. Altogether, the strains that have one of the original 25 sequence forms include 98 A. baumannii (24 from our strains) and 5 A. nosocomialis (3 from our strains), whereas 32 genomes from 12 species other than A. baumannii or A. nosocomialis, all have new sequence forms. One of the 25 serovar type sequences is found to be in European clone I (EC I), 2 are in EC II but none in EC III. The public genome strains add an additional 52 new sequence forms, and also bring the number found in EC I to 5, in EC II to 9 and in EC III to 2.
antigen, structure, Acinetobacter baumannii, gene cluster, glycosyltransferase, serotyping, genome, surface polysaccharide, polysaccharide antigen
NCBI PubMed ID: 23922982Publication DOI: 10.1371/journal.pone.0070329Journal NLM ID: 101285081Publisher: San Francisco, CA: Public Library of Science
Correspondence: Peter R. Reeves
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China, Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands, School of Molecular Bioscience, University of Sydney, Sydney, Australia
Methods: PCR, DNA sequencing, DNA techniques, genetic methods
- Article ID: 5791
Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.
polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component
Publication DOI: 10.1016/B978-0-12-819475-1.00005-5Publisher: Elsevier
Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
Editors: Barchi J, Kamerling H
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
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7. Compound ID: 731
|
R-3HOBut-(1-3)-b-D-Fucp3N-(1-3)-a-D-GalpNAc-(1-3)-b-D-GalpNAc-(1-3)-+
|
-3)-b-D-GalpNAc-(1-4)-a-D-Galp-(1-3)-D-Gro-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_151528,IEDB_153207,IEDB_153208,IEDB_190606,IEDB_885822,SB_21,SB_25,SB_7
The structure is contained in the following publication(s):
- Article ID: 194
Vinogradov EV, Pantophlet R, Dijkshoorn L, Brade L, Holst O, Brade H "Structural and serological characterisation of two O-specific polysaccharides of Acinetobacter" -
European Journal of Biochemistry 239 (1996) 602-610
Extraction of dry bacteria of Acinetobacter strain 34 (DNA group 2) or Acinetobacter strain 108 (DNA group 13) by phenol/water yielded a polymer that was identified by means of serological studies and fatty acid analysis as S-form lipopolysaccharide. Degradation of the lipopolysaccharides of strains 34 and 108 in 1% acetic acid and 5% acetic acid, respectively, and gel-permeation chromatography gave the respective O-antigenic polysaccharides, the structures of which were determined, by compositional analysis and NMR spectroscopy of the polysaccharide, as [Sequence: see text] for strain 108, where D-Fucp3NBuOH represents 3-[(R)-3-hydroxybutyramido] -3,6-dideoxy-D-galactose and D-GalpANAc represents 2-acetamido-2-deoxy-D-galacturonic acid. Both structures were specifically recognised in Western blots by polyclonal rabbit antisera and there was no cross-reaction between these two structures.
Lipopolysaccharide, NMR, Acinetobacter, serology, Western blot
NCBI PubMed ID: 8774703Publication DOI: 10.1111/j.1432-1033.1995.899_3.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: Division of Biochemical Microbiology, Center for Medicine and Biosciences, Research Center Borstel, Germany, Department of Medical Microbiology, Leiden University Hospital, Leiden, The Netherlands
Methods: NMR-2D, NMR, composition analysis
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8. Compound ID: 935
|
b-D-Galf-(1-3)-+
|
-5)-b-D-Galf-(1-3)-b-D-Galp-(1-4)-b-D-GalpNAc-(1-3)-a-D-Galp-(1-2)-D-Rib-ol-(5-P-
|
b-D-Galp-(1-6)-+ |
Show graphically |
Structure type: polymer chemical repeating unit
Trivial name: CPS10A
Compound class: CPS
Contained glycoepitopes: IEDB_114703,IEDB_130648,IEDB_136044,IEDB_136095,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_151528,IEDB_190606,IEDB_591403,SB_165,SB_166,SB_187,SB_195,SB_21,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 274
Jones C "Full assignment of the NMR spectrum of the capsular polysaccharide from Streptococcus pneumoniae serotype 10A" -
Carbohydrate Research 269(1) (1995) 175-181
NMR, capsular, polysaccharide, serotype, Streptococcus, Streptococcus pneumoniae, capsular polysaccharide, assignment
NCBI PubMed ID: 7773987Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Laboratory for Molecular Structure, National Institute for Biological Standards and Control, South Mimms, UK
Methods: NMR-2D, NMR
- Article ID: 301
Lee CH, Frasch CE "Quantification of bacterial polysaccharides by the purpald assay: Measurement of periodate-generated formaldehyde from glycol in the repeating unit" -
Analytical Biochemistry 296(1) (2001) 73-82
We have adapted the purpald assay for measurement of bacterial polysaccharides (PS) containing substituted and/or unsubstituted glycol (SG or UG) in residues such as glycerol, ribitol, arabinitol, furanosyl galactose, and sialyl. For the purpald assay of UG-containing PS, 50 microL of PS samples was consecutively reacted with 50 microL of 16 mM NaIO4 for 20 min, 50 microL of 136 mM purpald reagent in 2 N NaOH for 20 min, and 50 microL of 64 mM NaIO4 for 20 min in a 96-well tissue culture plate followed by a measurement of absorbance at 550 nm with a plate reader. For SG-containing PS, conversion of SG to UG with 25 micro;L of 0.3 N NaOH, 1 h at room temperature for de-O-acetylation followed by 25 microL of 0.6 M H2SO4, 1 h at 80 degrees C for acid hydrolysis of PS precedes the periodate treatment in the purpald assay. The concentration of the samples can be calculated from the sample absorbance and the reference standard curve constructed from the reference concentrations of the same PS (well-characterized) and their corresponding absorbance values assayed in the same plate. The purpald assay provides a tool in addition to the existing ones for the measurement of glycol-containing PS. Among the usefulness of this method are the determinations of the glycerol content in the phospho-glycerol-containing PS and the SG and UG contents and structural integrity in PS and conjugate vaccines.
repeating unit, bacterial polysaccharides, quantification
NCBI PubMed ID: 11520034Publication DOI: 10.1006/abio.2001.5230Journal NLM ID: 0370535Publisher: Academic Press
Institutions: Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, OVRR, CBER, FDA, 8800 Rockville Pike, Bethesda, MD, USA
Methods: purpald assay measurement
- Article ID: 507
Pujar NS, Huang NF, Daniels CL, Dieter L, Gayton MG, Lee AL "Base hydrolysis of phosphodiester bonds in pneumococcal polysaccharides" -
Biopolymers 75(1) (2004) 71-84
A comprehensive study of the base hydrolysis of all phosphodiester bond-containing capsular polysaccharides of the 23-valent pneumococcal vaccine is described here. Capsular polysaccharides from serotypes 6B, 10A, 17F, 19A, 19F, and 20 contain a phosphodiester bond that connects the repeating units in these polysaccharides (also referred to as backbone phosphodiester bonds), and polysaccharides from serotypes 11A, 15B, 18C, and 23F contain a phosphodiester bond that links a side chain to their repeating units. Molecular weight measurements of the polysaccharides, using high performance size exclusion chromatography with tandem multiangle laser light scattering and refractive index detection, was used to evaluate the kinetics of hydrolysis. The measurement of molecular weight provides a high degree of sensitivity in the case of small extents of reaction, thus allowing reliable measurements of the kinetics over short times. Pseudo-first-order rate constants for these polysaccharides were estimated using a simple model that accounts for the polydispersity of the starting sample. It was found that the relative order of backbone phosphodiester bond instability due to base hydrolysis was 19A > 10A > 19F > 6B > 17F, 20. Degradation of side-chain phosphodiester bonds was not observed, although the high degree of sensitivity in measurements is lost in this case, due to the low contribution of the side chains to the total polysaccharide molecular weight. In comparison with literature data on pneumococcal polysaccharide 6A, 19A was found to be the more labile, and hence appears to be the most labile pneumococcal polysaccharide studied to date. The rate of hydrolysis increased at higher pH and in the presence of divalent cation, but the extent was lower than expected based on similar data on RNA. Finally, the differences in the phosphodiester bond stabilities were analyzed by considering stereochemical factors in these polysaccharides. These results also provide a framework for evaluation of molecular integrity of phosphodiester-bond-containing polysaccharides in different solution conditions. Copyright 2004 Wiley Periodicals, Inc. Biopolymers, 2004
base hydrolysis, phosphodiester bond, pneumococcal polysaccharide
NCBI PubMed ID: 15307199Journal NLM ID: 0372525Publisher: Wiley Interscience
Correspondence: hari_pujar@merck.com
Institutions: Merck Research Laboratories, Merck & Co., West Point, PA 19486
- Article ID: 1347
Abeygunawardana C, Williams TC, Sumner JS, Hennessey JP "Development and validation of an NMR-based identity assay for bacterial polysaccharides" -
Analytical Biochemistry 279(2) (2000) 226-240
A method utilizing NMR spectroscopy has been developed to confirm the identity of bacterial polysaccharides used to formulate a polyvalent pneumococcal polysaccharide vaccine. The method is based on 600 MHz proton NMR spectra of individual serotype-specific polysaccharides. A portion of the anomeric region of each spectrum (5.89 to 4.64 ppm) is compared to spectra generated for designated reference samples for each polysaccharide of interest. The selected region offers a spectral window that is unique to a given polysaccharide and is sensitive to any structural alteration of the repeating units. The similarity of any two spectral profiles is evaluated using a correlation coefficient (rho), where rho >/= 0.95 between a sample and reference profile indicates a positive identification of the sample polysaccharide. This method has been shown to be extremely selective in its ability to discriminate between serotype-specific polysaccharides, some of which differ by no more than a single glycosidic linkage. Furthermore, the method is rapid and does not require extensive sample manipulations or pretreatments. The method was validated as a qualitative identity assay and will be incorporated into routine quality control testing of polysaccharide powders to be used in preparation of the polyvalent pneumococcal vaccine PNEUMOVAX 23. The specificity and reproducibility of the NMR-based identity assay is superior to the currently used colorimetric assays and can be readily adapted for use with other bacterial polysaccharide preparations as well.
NMR, Bacterial, polysaccharide, Bacterial polysaccharide, polysaccharides, bacterial polysaccharides, assay, development, identity assay, method development, validation
NCBI PubMed ID: 10706792Publication DOI: 10.1006/abio.1999.447Journal NLM ID: 0370535Publisher: Academic Press
Correspondence: abey@merck.com
Institutions: Bioprocess and Bioanalytical Research, Merck Research Laboratories, West Point, Pensylvania, USA
Methods: NMR
- Article ID: 1556
Pujar NS, Huang NF, Daniels CL, Dieter L, Gayton MG, Lee AL "Erratum: Base hydrolysis of phosphodiester bonds in pneumococcal polysaccharides" -
Biopolymers 77(6) (2005) 378-379
No abstract
polysaccharide, Streptococcus, Research, hydrolysis, polysaccharides, phosphodiester, pneumococcal, PDF, P, pneumococcal polysaccharides
NCBI PubMed ID: 15761954Journal NLM ID: 0372525Publisher: Wiley Interscience
Institutions: WP17-301, P. O. Box 4, Merck Research Laboratories, Merck & Co., West Point, PA 19486
- Article ID: 3966
Yang J, Shelat NY, Bush CA, Cisar JO "Structure and molecular characterization of Streptococcus pneumoniae capsular polysaccharide 10F by carbohydrate engineering in Streptococcus oralis" -
Journal of Biological Chemistry 285(31) (2010) 24217-24227
Although closely related at the molecular level, the capsular polysaccharide (CPS) of serotype 10F Streptococcus pneumoniae and coaggregation receptor polysaccharide (RPS) of Streptococcus oralis C104 have distinct ecological roles. CPS prevents phagocytosis of pathogenic S. pneumoniae, whereas RPS of commensal S. oralis functions as a receptor for lectin-like adhesins on other members of the dental plaque biofilm community. Results from high resolution NMR identified the recognition region of S. oralis RPS (i.e. Galfβ1-6GalNAcβ1-3Galα) in the hexasaccharide repeat of S. pneumoniae CPS10F. The failure of this polysaccharide to support fimbriae-mediated adhesion of Actinomyces naeslundii was explained by the position of Galf, which occurred as a branch in CPS10F rather than within the linear polysaccharide chain, as in RPS. Carbohydrate engineering of S. oralis RPS with wzy from S. pneumoniae attributed formation of the Galf branch in CPS10F to the linkage of adjacent repeating units through sub terminal GalNAc in Galfβ1-6GalNAcβ1-3Galα rather than through terminal Galf, as in RPS. A gene (wcrD) from serotype 10A S. pneumoniae was then used to engineer a linear surface polysaccharide in S. oralis that was identical to RPS except for the presence of a β1-3 linkage between Galf and GalNAcβ1-3Galα. This polysaccharide also failed to support adhesion of A. naeslundii, thereby establishing the essential role of β1-6-linked Galf in recognition of adjacent GalNAcβ1-3Galα in wild-type RPS. These findings, which illustrate a molecular approach for relating bacterial polysaccharide structure to function, provide insight into the possible evolution of S. oralis RPS from S. pneumoniae CPS.
NMR, structure, Streptococcus pneumoniae, capsular polysaccharide, Bacterial Adhesion, biofilms, Streptococcus oralis
NCBI PubMed ID: 20507989Publication DOI: 10.1074/jbc.M110.123562Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: john.cisar@nih.gov
Institutions: Oral Infection and Immunity Branch, NIDCR, National Institutes of Health, Bethesda, MD, USA
Methods: 13C NMR, 1H NMR, NMR-2D, GC-MS, HF solvolysis, NMR-1D, serological methods, genetic methods, immunoblotting
- Article ID: 4828
Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP, Jones C, Konradsen HB, Nahm MH "Pneumococcal Capsules and Their Types: Past, Present, and Future" -
Clinical Microbiology Reviews 28(3) (2015) 871-899
Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.
serotype, Streptococcus pneumoniae, vaccines, Pneumococcal Capsules
NCBI PubMed ID: 26085553Publication DOI: 10.1128/CMR.00024-15Journal NLM ID: 8807282Publisher: Washington, DC: American Society for Microbiology
Correspondence: Moon H. Nahm
Institutions: Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA, Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Wentworthville, New South Wales, Australia, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia, Division of Infectious Disease, Department of Internal Medicine, Korea University Guro Hospital, Seoul, South Korea, SSI Diagnostica, Division of Microbiology and Diagnostics, Statens Serum Institut, Copenhagen, Denmark, Pneumonia Program Strategy Team, Bill & Melinda Gates Foundation, Seattle, Washington, USA, Laboratory for Molecular Structure, NIBSC, South Mimms, Herts, United Kingdom, Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Article ID: 4836
Berti F, Ravenscroft N "Characterization of Carbohydrate Vaccines by NMR Spectroscopy" -
Methods in Molecular Biology 1331 (2015) 189-209
Physicochemical techniques are a powerful tool for the structural characterization of carbohydrate-based vaccines. High-field Nuclear Magnetic Resonance (NMR) spectroscopy has been established as an extremely useful and robust method for tracking the industrial manufacturing process of these vaccines from polysaccharide bulk antigen through to the final formulation. Here, we describe the use of proton NMR for structural identity and conformity testing of carbohydrate-based vaccines.
carbohydrates, capsular polysaccharide, antigens, nuclear magnetic resonance spectroscopy, vaccines
NCBI PubMed ID: 26169742Publication DOI: 10.1007/978-1-4939-2874-3_12Journal NLM ID: 9214969Publisher: Springer
Correspondence: francesco.x.berti@gsk.com
Institutions: Research, GSK Vaccines, Via Fiorentina 1, 53100, Siena, Italy
- Article ID: 5473
Zou W, Li J, Vinogradov E, Cox A "Removal of cell wall polysaccharide in pneumococcal capsular polysaccharides by selective degradation via deamination" -
Carbohydrate Polymers 218 (2019) 199-207
Pneumococcal cell wall polysaccharide (C-PS), a contaminant in pneumococcal capsular polysaccharide (Pn-PS) vaccines is degraded by mild deamination of the 4-amino-2-acetamido-2,4,6-tri-deoxy-galactose (AAT) in C-PS, which was carried out by addition of 5% aqueous sodium nitrite to a solution of polysaccharide in 5% aqueous acetic acid. Glycosidic linkage and functional groups such as O-acetates, phosphodiesters, and pyruvates were preserved under the conditions. The small fragments from degraded C-PS were removed by ultrafiltration or dialysis to provide essentially C-PS free Pn-PS. Because of the presence of AAT in its structure the deamination is not suitable for the purification of type 1 Pn-PS. Meanwhile, the mass and NMR spectroscopic analysis on the deamination products suggests that both type 1 Pn-PS and C-PS degraded following a major pathway of 5,4-hydride shift, cleavage of AAT O5-C1 bond, C1 hemiacetal formation, and its hydrolysis to release neighboring GalA- in type 1 Pn-PS and GalNAc(6-O-PCho)- in C-PS
mechanism, degradation, deamination, cell wall polysaccharide, pneumococcal capsular polysaccharide
NCBI PubMed ID: 31221321Publication DOI: 10.1016/j.carbpol.2019.03.070Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: W. Zou
Institutions: Human Health Therapeutic Research Center, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
Methods: 13C NMR, 1H NMR, gel filtration, sugar analysis, MS/MS, MS, dialysis, SEC-HPLC, ultrafiltration, mild deamination
- Article ID: 5769
Ganaie F, Saad JS, McGee L, van Tonder AJ, Bentley SD, Lo SW, Gladstone RA, Turner P, Keenan JD, Breiman RF, Nahm MH "A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus" -
mBio 11(3) (2020)
Streptococcus pneumoniae (pneumococcus) is a major human pathogen producing structurally diverse capsular polysaccharides. Widespread use of highly successful pneumococcal conjugate vaccines (PCVs) targeting pneumococcal capsules has greatly reduced infections by the vaccine types but increased infections by nonvaccine serotypes. Herein, we report a new and the 100th capsule type, named serotype 10D, by determining its unique chemical structure and biosynthetic roles of all capsule synthesis locus (cps) genes. The name 10D reflects its serologic cross-reaction with serotype 10A and appearance of cross-opsonic antibodies in response to immunization with 10A polysaccharide in a 23-valent pneumococcal vaccine. Genetic analysis showed that 10D cps has three large regions syntenic to and highly homologous with cps loci from serotype 6C, serotype 39, and an oral streptococcus strain (S. mitis SK145). The 10D cps region syntenic to SK145 is about 6 kb and has a short gene fragment of wciNalpha at the 5' end. The presence of this nonfunctional wciNalpha fragment provides compelling evidence for a recent interspecies genetic transfer from oral streptococcus to pneumococcus. Since oral streptococci have a large repertoire of cps loci, widespread PCV usage could facilitate the appearance of novel serotypes through interspecies recombination.IMPORTANCE The polysaccharide capsule is essential for the pathogenicity of pneumococcus, which is responsible for millions of deaths worldwide each year. Currently available pneumococcal vaccines are designed to elicit antibodies to the capsule polysaccharides of the pneumococcal isolates commonly causing diseases, and the antibodies provide protection only against the pneumococcus expressing the vaccine-targeted capsules. Since pneumococci can produce different capsule polysaccharides and therefore reduce vaccine effectiveness, it is important to track the appearance of novel pneumococcal capsule types and how these new capsules are created. Herein, we describe a new and the 100th pneumococcal capsule type with unique chemical and serological properties. The capsule type was named 10D for its serologic similarity to 10A. Genetic studies provide strong evidence that pneumococcus created 10D capsule polysaccharide by capturing a large genetic fragment from an oral streptococcus. Such interspecies genetic exchanges could greatly increase diversity of pneumococcal capsules and complicate serotype shifts.
Streptococcus pneumoniae, capsule, vaccine, genetic exchange
NCBI PubMed ID: 32430472Publication DOI: 10.1128/mBio.00937-20Journal NLM ID: 101519231Publisher: Washington, DC: American Society for Microbiology
Correspondence: mnahm@uabmc.edu
Institutions: Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom, Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom, Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, Department of Ophthalmology, University of California, San Francisco, California, USA, Emory Global Health Institute, Emory University, Atlanta, Georgia, USA
Methods: 13C NMR, 1H NMR, NMR-2D, ELISA, serological methods, genetic methods, bioinformatic analysis, opsonophagocytosis assay
- Article ID: 5791
Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.
polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component
Publication DOI: 10.1016/B978-0-12-819475-1.00005-5Publisher: Elsevier
Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
Editors: Barchi J, Kamerling H
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
- Article ID: 6073
Javed J, Mandal PK "Bacterial surface capsular polysaccharides from Streptococcus pneumoniae: A systematic review on structures, syntheses, and glycoconjugate vaccines" -
Carbohydrate Research 502 (2021) 108277
The polysaccharide capsule of Streptococcus pneumoniae constitutes the outermost surface structure of the organism and plays a critical role in virulence. The capsule is the target of current pneumococcal vaccines and glycoconjugates and has important medical and industrial applications. Widespread use of these vaccines is driving changes in serotype prevalence in disease. A massive array of sugars and glycosidic linkages experienced with complete diversity of potential polysaccharide structures. However, it is impossible to collect a sufficient quantity of glycan antigens for the preparation of CPS-based glycoconjugate vaccines from natural sources with high purity and for thorough biological evaluation. So nowadays, the development of a chemical synthetic strategy and their conjugation with a carrier protein to form synthetic glycoconjugate vaccines has been used to gain access on a large scale. This review provides a comprehensive summary of structures, synthesis as well as recent development of synthetic glycoconjugate vaccines, which will support research and may benefit the glycochemical and medical sciences.
synthesis, Streptococcus pneumoniae, glycoconjugate vaccines, polysaccharides, Pneumococcal Infections
NCBI PubMed ID: 33743443Publication DOI: 10.1016/j.carres.2021.108277Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: P.K. Mandal
Institutions: Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow, 226 031, India, Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
- Article ID: 6306
Richardson NI, Kuttel MM, Ravenscroft N "Modeling of pneumococcal serogroup 10 capsular polysaccharide molecular conformations provides insight into epitopes and observed cross-reactivity" -
Frontiers in Molecular Biosciences 9 (2022) 961532
Streptococcus pneumoniae is an encapsulated gram-negative bacterium and a significant human pathogen. The capsular polysaccharide (CPS) is essential for virulence and a target antigen for vaccines. Although widespread introduction of pneumococcal conjugate vaccines (PCVs) has significantly reduced disease, the prevalence of non-vaccine serotypes has increased. On the basis of the CPS, S. pneumoniae serogroup 10 comprises four main serotypes 10A, 10B, 10C, and 10F; as well as the recently identified 10D. As it is the most prevalent, serotype 10A CPS has been included as a vaccine antigen in the next generation PCVs. Here we use molecular modeling to provide conformational rationales for the complex cross-reactivity reported between serotypes 10A, 10B, 10C, and 10F anti-sera. Although the highly mobile phosphodiester linkages produce very flexible CPS, shorter segments are conformationally defined, with exposed β-D-galactofuranose (β DGalf) side chains that are potential antibody binding sites. We identify four distinct conformational epitopes for the immunodominant β DGalf that assist in rationalizing the complex asymmetric cross-reactivity relationships. In particular, we find that strongly cross-reactive serotypes share common epitopes. Further, we show that human intelectin-1 has the potential to bind the exposed exocyclic 1,2-diol of the terminal β DGalf in each serotype; the relative accessibility of three- or six-linked β DGalf may play a role in the strength of the innate immune response and hence serotype disease prevalence. In conclusion, our modeling study and relevant serological studies support the inclusion of serotype 10A in a vaccine to best protect against serogroup 10 disease.
capsular polysaccharide, molecular modeling, carbohydrate epitopes, cross-protection, S.pneumoniae, serogroup 10, vaccine antigen
NCBI PubMed ID: 36003080Publication DOI: 10.3389/fmolb.2022.961532Journal NLM ID: 101653173Publisher: Lausanne: Frontiers Media S.A.
Correspondence: N. Ravenscroft
Institutions: Department of Computer Science, University of Cape Town, Cape Town, South Africa, Department of Chemistry, University of Cape Town, Cape Town, South Africa
Methods: conformation analysis, MD simulations, binding assays, data analysis, convergence, chain flexibility
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9. Compound ID: 991
|
b-D-GalpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Glcp-(1--/inner core-lipid A/ |
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Structure type: oligomer
Aglycon: inner core-lipid A
Compound class: LOS
Contained glycoepitopes: IEDB_130646,IEDB_130648,IEDB_130697,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_137776,IEDB_1391966,IEDB_140108,IEDB_140110,IEDB_140122,IEDB_141794,IEDB_141807,IEDB_142351,IEDB_142487,IEDB_142488,IEDB_146664,IEDB_149144,IEDB_151531,IEDB_190606,IEDB_983931,SB_145,SB_165,SB_166,SB_173,SB_187,SB_192,SB_195,SB_21,SB_30,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 272
John CM, Schneider H, Griffiss JM "Neisseria gonorrhoeae that infect men have lipooligosaccharides with terminal N-acetyllactosamine repeats" -
Journal of Biological Chemistry 274(2) (1999) 1017-1025
Infectious Neisseria gonorrhoeae make relatively large lipooligosaccharides (LOS) that structurally resemble human glycosphingolipids. MS11mkC is an LOS variant of N. gonorrhoeae strain MS11 which was isolated from men at the onset of dysuria (Schneider, H., Griffiss, J. M., Boslego, J. W., Hitchcock, P. J., Zahos, K. M., and Apicella, M. A. (1991) J. Exp. Med. 174, 1601-1605). Delayed extraction matrix-assisted laser desorption and ionization and electrospray ionization mass spectrometry of O-deacylated MS11mkC LOS produced ions consistent with known LOS which have lacto-N-neotetraose (Gal β1→4 GlcNAc β1→3 Gal β1→4 Glc; paraglobosyl; monoclonal antibodies (mAbs) 1B2(+) and 06B4(+)) and GalNAc→lacto-N-neotetraose (gangliosyl; mAb 1-1-M+) oligosaccharides. Ion peaks for a larger LOS which also bound mAb 1B2 indicated the addition of a hexose (+162 Da) to gangliosyl LOS or the addition of a hexose and a N-acetylhexosamine (+365 Da) to paraglobosyl LOS. Analysis of HF-treated and O-deacylated LOS revealed three major components present in a phosphoethanolamine (PEA)0 and a PEA1 series. Digestion of MS11mkC LOS by β-N-acetylhexosaminidase and β-galactosidase, alone and sequentially, combined with mAb binding patterns, confirmed the presence of a nonreducing terminal repeating LacNAc ((Gal β1→4 GlcNAc)2) on the largest LOS, rather than a parallel oligosaccharide structure.
Neisseria, Gonorrhoeae, Neisseria gonorrhoeae, lipooligosaccharides, N-acetyllactosamine
NCBI PubMed ID: 9873046Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: cjohn@vacom.ucsf.edu.net
Institutions: Centre for Immunochemistry and the Department of Laboratory Medicine, University of California, San Francisco, California 94121 and the Department of Bacterial Diseases, Walter Reed Army Institute of Research, Washington, D. C. 20307.
Methods: ESI-MS, MALDI-MS
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10. Compound ID: 1048
|
a-D-Galp-(1-2)-+
|
Gro-(2--P--3)--b-D-Galp-(1-4)-+
|
-6)-b-D-GalpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Glcp-(1- |
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Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_130648,IEDB_131186,IEDB_135818,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_146664,IEDB_151528,IEDB_167072,IEDB_190606,IEDB_742245,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_21,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 301
Lee CH, Frasch CE "Quantification of bacterial polysaccharides by the purpald assay: Measurement of periodate-generated formaldehyde from glycol in the repeating unit" -
Analytical Biochemistry 296(1) (2001) 73-82
We have adapted the purpald assay for measurement of bacterial polysaccharides (PS) containing substituted and/or unsubstituted glycol (SG or UG) in residues such as glycerol, ribitol, arabinitol, furanosyl galactose, and sialyl. For the purpald assay of UG-containing PS, 50 microL of PS samples was consecutively reacted with 50 microL of 16 mM NaIO4 for 20 min, 50 microL of 136 mM purpald reagent in 2 N NaOH for 20 min, and 50 microL of 64 mM NaIO4 for 20 min in a 96-well tissue culture plate followed by a measurement of absorbance at 550 nm with a plate reader. For SG-containing PS, conversion of SG to UG with 25 micro;L of 0.3 N NaOH, 1 h at room temperature for de-O-acetylation followed by 25 microL of 0.6 M H2SO4, 1 h at 80 degrees C for acid hydrolysis of PS precedes the periodate treatment in the purpald assay. The concentration of the samples can be calculated from the sample absorbance and the reference standard curve constructed from the reference concentrations of the same PS (well-characterized) and their corresponding absorbance values assayed in the same plate. The purpald assay provides a tool in addition to the existing ones for the measurement of glycol-containing PS. Among the usefulness of this method are the determinations of the glycerol content in the phospho-glycerol-containing PS and the SG and UG contents and structural integrity in PS and conjugate vaccines.
repeating unit, bacterial polysaccharides, quantification
NCBI PubMed ID: 11520034Publication DOI: 10.1006/abio.2001.5230Journal NLM ID: 0370535Publisher: Academic Press
Institutions: Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, OVRR, CBER, FDA, 8800 Rockville Pike, Bethesda, MD, USA
Methods: purpald assay measurement
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11. Compound ID: 1266
|
a-Neup-(2-3)-+
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b-D-GalpNAc-(1-4)-b-D-Galp-(1-4)-b-D-GalpNAc-(1-3)-b-D-Galp-(1-3)-D-GalNAc-ol |
Show graphically |
Structure type: oligomer
Contained glycoepitopes: IEDB_130648,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_190606,SB_165,SB_166,SB_187,SB_195,SB_21,SB_25,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 397
Torgov VI, Shashkov AS, Jann B, Jann K "NMR reinvestigation of two N-acetylneuraminic acid-containing O-specific polysaccharides (O56 and O24) of Escherichia coli" -
Carbohydrate Research 272(1) (1995) 73-90
Structures for the N-acetylneuraminic acid (Neu5Ac)-containing O56 and O24 polysaccharides of Escherichia coli have been reported previously. During these studies unusual chemical shifts had been observed for the NMR signals for H-3eq and C-3 of the Neu5Ac residues of both polysaccharides. In further pursuing this phenomenon, we have reinvestigated the O56 and O24 polysaccharides as well as derived oligosaccharides by one- and two-dimensional NMR spectroscopy. The results showed that structures of both polysaccharides (PSs) had to be modified and formulated as [formula: see text] 2D ROESY spectra revealed a strong NOE between H-3eq of Neu5Ac and the protons of the side-chain sugar (H-3 and H-5 of α-D-Galp in the O56 PS and H-3 of α-D-Glcp in the O24 PS) and also between H-3ax of Neu5Ac and H-3 of β-D-Glcp in the main chain. This indicated a close spatial association of the seven-linked α-Neu5Ac and the side-chain residues α-D-Galp (O56 PS) and α-D-Glcp (O25 PS), respectively. The strong long-range spatial contacts caused the unusual chemical shifts of H-3eq and C-3 of Neu5Ac.
Escherichia coli, NMR spectroscopy, polysaccharide structure, 024 and 056 antigens
NCBI PubMed ID: 7544238Publication DOI: 10.1016/0008-6215(95)00041-QJournal NLM ID: 0043535Publisher: Elsevier
Correspondence: torgov@ioc.ac.ru
Institutions: Max-Planck-Institut für Immunbiologie, Freiburg, Germany
Methods: NMR-2D, NMR, sugar analysis, Smith degradation
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12. Compound ID: 1279
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115013,IEDB_130645,IEDB_130648,IEDB_134627,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_147450,IEDB_149558,IEDB_151528,IEDB_190606,IEDB_918314,SB_165,SB_166,SB_187,SB_195,SB_21,SB_23,SB_24,SB_7,SB_8,SB_87,SB_88
The structure is contained in the following publication(s):
- Article ID: 405
Vinion-Dubiel AD, Goldberg JB "Lipopolysaccharide of Burkholderia cepacia complex" -
Journal of Endotoxin Research 9(4) (2003) 201-213
Burkholderia cepacia complex (Bcc) is a group of phenotypically similar, genetically distinct bacteria that are beneficial to the environment but can also cause severe human infections. Bcc are being exploited for use as bioremediation agents and as a way to combat agricultural plant diseases. However, Bcc can cause lung infections in patients with chronic granulomatous disease or cystic fibrosis often resulting in mortality of these patients. Since it is unclear what bacterial components are necessary for causing human infections, studies of Bcc have focused on identifying putative virulence factors. As in other Gram-negative bacteria, the lipopolysaccharide (LPS) of Bcc induces a strong immune response that can contribute to host cell damage. The unusual structure of Bcc LPS lowers the anionic charge of the Bcc cell surface, which inhibits the binding and subsequent effects of cationic antibiotics. These distinguishing features include the substitution of a Ko for a Kdo residue in the inner core oligosaccharide and Ara4N residues bound to phosphates of the lipid A backbone. The structures of O antigen subunits and the consequent serotypes will also be discussed, with particular reference to the O antigen biosynthetic loci of two Bcc strains.
Lipopolysaccharide, structure, Burkholderia, Burkholderia cepacia, O-antigen, complex, endotoxin, Re
NCBI PubMed ID: 12935351Publication DOI: 10.1177/09680519030090040101Journal NLM ID: 9433350Publisher: Maney Publishing
Institutions: Department of Microbiology, University of Virginia Health Sciences Center, Charlottesville, VA 22908-0734, USA
- Article ID: 640
Gaur D, Wilkinson SG "Lipopolysaccharide from Burkholderia vietnamiensis strain LMG 6999 contains two polymers identical to those present in the reference strain for Burkholderia cepacia serogroup O4" -
FEMS Microbiology Reviews 295 (1997) 183-188
Lipopolysaccharide was isolated from strain LMG 6999 of Burkholderia vietnamiensis. Degradative and NMR spectroscopic studies established the presence of two polymeric fractions based on the following trisaccharide repeating units: I:[-3)aDGalp(1-3)bDGalp(1-3)[Ac(1-2)]bDGalpN(1-]; II:[-3)[Ac(1-2)]aDGalpN(1-3)[Ac(1-2)]bDGalpN(1-4)aLRhap(1-]. The same polymers have previously been found together in lipopolysaccharide from the reference strain for Burkholderia cepacia serogroup O4 and, individually, in those from B. cepacia serogroups C (I) and A (II).
Lipopolysaccharide, LPS, structure, strain, polysaccharide, Burkholderia, Burkholderia cepacia, polymer, O-specific, O-specific polysaccharide, serogroup, reference, Polymers, Burkholderia vietnamiensis
NCBI PubMed ID: 9418254Journal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: S.G.Wilkinson@chem.hull.ac.uk
Institutions: School of Chemistry, University of Hull, Hull HU6 7RX, UK
Methods: methylation, NMR-2D, NMR, Smith degradation, GPC
- Article ID: 783
Cox AD, Taylor CJ, Anderson AJ, Perry MB, Wilkinson SG "Structures of the two polymers present in the lipopolysaccharide of Burkholderia_Pseudomonas cepacia serogroup O4" -
European Journal of Biochemistry 231 (1995) 784-789
Like several other strains of Burkholderia_Pseudomonas cepacia, the reference strain for serogroup O4 in the French typing scheme [Heidt, A., Monteil, H. & Richard, C. (1983) J. Clin. Microbiol. 18, 738-740] produces a lipopolysaccharide containing two distinct polymers. Attempts to separate the polymers chromatographically were unsuccessful, but the periodate-resistant major polymer could be isolated by application of the Smith degradation technique to the mixture. By means of chemical and NMR spectroscopic analysis, the following structure could be assigned to the repeating unit of the major polymer: →3)-α-D-Galp-(1→3)-β-D-Galp-(1→3)-β-D-GalpNAc-(1→. The following structure of the repeating unit of the minor polymer was established from similar studies of its degradation product, resulting from the oxidation of L-rhamnose (Rha), and of the original mixture: →3)-α-D-GalpNAc-(1→3)-β-D-GalpNAc-(1→4)-α-L-Rhap-(1→. Individually, the polymers have recently been found in related strains of B. cepacia. The minor polymer was identified as the O-antigen in serotype A of a Canadian typing scheme [Beynon, L. M. & Perry, M. B. (1993) Biochem. Cell Biol. 71, 417-420], and the major polymer in serotype C of a Japanese typing scheme [Paramonov, N. A., Shashkov, A. S., Knirel, Y. A., Soldatkina, M. A. & Zakharova, I. Y. (1994) Bioorg. Khim. 20, 984-993]. In the case of the O4 strain studied here, both polymers were produced under a variety of growth conditions.
Lipopolysaccharide, LPS, structure, Burkholderia, Burkholderia cepacia, O-antigen, Pseudomonas, polymer, serogroup, Polymers, Pseudomonas cepacia
NCBI PubMed ID: 7544286Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, ON, Canada.
Methods: NMR, sugar analysis, Smith degradation
- 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: 7533007Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 1891
Paramonov NA, Shashkov AS, Knirel YA, Soldatkina MA, Zakharova IY "Antigenic polysaccharides of bacteria. 39. Structure of O-specific polysaccharides of Pseudomonas cepacia serogroups C, I, O1 and O4" -
Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 20(8-9) (1994) 984-993
Like some Pseudomonas cepacia serogroups studied earlier, serogroups C, I (Nakamura), O1 and O4 (Heidt) are characterized by the presence of at least two structurally different O-antigenic polysaccharide chains in cell-wall lipopolysaccharides. On the basis of acid hydrolysis, methylation, 1H- and 13C-NMR spectroscopy, including computer-assisted 13C-NMR-based analysis, the complete structures of the predominant polysaccharides of serogroups I (I), C and O4 (III) and the minor polysaccharides of serogroups I (II) and O1 (V) were established, and the structure of the predominant polysaccharide of serogroup O1 (IV) established earlier (Cox A. D., Wilkinson S. G.@Carbohydr. Res. 1990. V. 195. No 2. P. 295-301) was confirmed.
NCBI PubMed ID: 7530009Journal NLM ID: 7804941Publisher: Moskva: Nauka
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow
Methods: 13C NMR, 1H NMR, NMR-2D
- 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_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 4616
Sigida EN, Fedonenko YP, Zdorovenko EL, Konnova SA, Shashkov AS, Ignatov VV, Knirel YA "Structure of repeating units of a polysaccharide(s) from the lipopolysaccharide of Azospirillum brasilense SR80" -
Carbohydrate Research 371 (2013) 40-44
A high-molecular mass polysaccharide fraction was obtained by mild acid hydrolysis of the lipopolysaccharide of diazotrophic rhizobacterium Azospirillum brasilense SR80 followed by GPC on Sephadex G-50 Superfine. Studies by composition and methylation analyses, Smith degradation, and 1D and 2D (1)H and (13)C NMR spectroscopy demonstrated the presence of two structurally distinct repeating units having the following structures: It seems likely, although not proved, that these are repeats of two distinct polysaccharides rather than they build blocks within the same polysaccharide chain. The former structure is new, whereas the latter is closely related to the O-polysaccharide structure of A. brasilense Jm6B2 established earlier, which differs in partial (~60%) 3-O-methylation of d-rhamnose only [Boiko, A. S.; Dmitrenok, A. S.; Fedonenko, Yu. P.; Zdorovenko, E. L.; Konnova, S. A.; Knirel, Y. A.; Ignatov, V. V. Carbohydr. Res.2012, 355, 92-95].
Lipopolysaccharide, Azospirillum brasilense, O-Polysaccharide structure
NCBI PubMed ID: 23500958Publication DOI: 10.1016/j.carres.2013.01.005Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: E.L. Zdorovenko
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov 410049, Russia
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, Smith degradation, composition analysis, GPC
- Article ID: 5143
Cloutier M, Muru K, Ravicoularamin G, Gauthier C "Polysaccharides from Burkholderia species as targets for vaccine development, immunomodulation and chemical synthesis" -
Natural Product Reports 35(12) (2018) 1251-1293
Burkholderia species are a vast group of human pathogenic, phytopathogenic, and plant- or environment-associated bacteria. B. pseudomallei, B. mallei, and B. cepacia complex are the causative agents of melioidosis, glanders, and cystic fibrosis-related infections, respectively, which are fatal diseases in humans and animals. Due to their high resistance to antibiotics, high mortality rates, and increased infectivity via the respiratory tract, B. pseudomallei and B. mallei have been listed as potential bioterrorism agents by the Centers for Disease Control and Prevention. Burkholderia species are able to produce a large network of surface-exposed polysaccharides, i.e., lipopolysaccharides, capsular polysaccharides, and exopolysaccharides, which are virulence factors, immunomodulators, major biofilm components, and protective antigens, and have crucial implications in the pathogenicity of Burkholderia-associated diseases. This review provides a comprehensive and up-to-date account regarding the structural elucidation and biological activities of surface polysaccharides produced by Burkholderia species. The chemical synthesis of oligosaccharides mimicking Burkholderia polysaccharides is described in detail. Emphasis is placed on the recent research efforts toward the development of glycoconjugate vaccines against melioidosis and glanders based on synthetic or native Burkholderia oligo/polysaccharides.
lipopolysaccharides, Burkholderia, capsular polysaccharides, Oligosaccharides, glycoconjugate vaccines, antigens, exopolysaccharides, surface polysaccharide, virulence factor, Biofilm, chemical synthesis, bioterrorism
Publication DOI: 10.1039/C8NP00046HJournal NLM ID: 8502408Publisher: London: Royal Society of Chemistry
Correspondence: charles.gauthier@iaf.inrs.ca
Institutions: INRS-Institut Armand-Frappier, Universite du Quebec, 531, boul. des Prairies, Laval, Canada
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13. Compound ID: 1295
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_141807,IEDB_151528,IEDB_151531,IEDB_190606,SB_21,SB_7
The structure is contained in the following publication(s):
- Article ID: 405
Vinion-Dubiel AD, Goldberg JB "Lipopolysaccharide of Burkholderia cepacia complex" -
Journal of Endotoxin Research 9(4) (2003) 201-213
Burkholderia cepacia complex (Bcc) is a group of phenotypically similar, genetically distinct bacteria that are beneficial to the environment but can also cause severe human infections. Bcc are being exploited for use as bioremediation agents and as a way to combat agricultural plant diseases. However, Bcc can cause lung infections in patients with chronic granulomatous disease or cystic fibrosis often resulting in mortality of these patients. Since it is unclear what bacterial components are necessary for causing human infections, studies of Bcc have focused on identifying putative virulence factors. As in other Gram-negative bacteria, the lipopolysaccharide (LPS) of Bcc induces a strong immune response that can contribute to host cell damage. The unusual structure of Bcc LPS lowers the anionic charge of the Bcc cell surface, which inhibits the binding and subsequent effects of cationic antibiotics. These distinguishing features include the substitution of a Ko for a Kdo residue in the inner core oligosaccharide and Ara4N residues bound to phosphates of the lipid A backbone. The structures of O antigen subunits and the consequent serotypes will also be discussed, with particular reference to the O antigen biosynthetic loci of two Bcc strains.
Lipopolysaccharide, structure, Burkholderia, Burkholderia cepacia, O-antigen, complex, endotoxin, Re
NCBI PubMed ID: 12935351Publication DOI: 10.1177/09680519030090040101Journal NLM ID: 9433350Publisher: Maney Publishing
Institutions: Department of Microbiology, University of Virginia Health Sciences Center, Charlottesville, VA 22908-0734, USA
- Article ID: 772
Cimino P, Corsaro MM, De Castro C, Evidente A, Marciano CE, Parrilli M, Sfalanga A, Surico G "Structural determination of the O-deacetylated O-chain of lipopolysaccharide from Burkholderia_Pseudomonas cepacia strain PVFi-5A" -
Carbohydrate Research 307 (1998) 333-341
On the basis of chemical degradation methods and one-and two-dimensional 1H and 13C NMR experiments the novel following structure was established for the O-deacetylated repeating unit of the O-chain of the main Burkholderia_Pseudomonas cepacia (strain PVFi-5A) lipopolysaccharide: →4)-β-D-GalpNAc-(1→3)-α-D-Galp-(1→6)-α-D-GlcpNAc-(1→.
Lipopolysaccharide, LPS, structure, strain, structural, polysaccharide, Burkholderia, Burkholderia cepacia, Pseudomonas, determination, structural determination, O-polysaccharide, O-specific, O-specific polysaccharide, Bacterial polysaccharide, O-chain, Pseudomonas cepacia
NCBI PubMed ID: 9675371Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: parrilli@unina.it
Institutions: Dipartimento di Chimica Organica e Biologica, Universita di Napoli Federico II, via Mezzocannone 16,I-80134 Napoli, Italy, Dipartimento di Scienze Chimico-Agrarie, Universita di Napoli Federico II, via Universita 100, I-80055 Portici, Italy, Istituto di Patologia e Zoologia Forestale e Agraria, Universita di Firenze, Piazzale delle Cascine 28, 50144 Firenze, Italy
Methods: methylation, NMR-2D, NMR, de-O-acylation, sugar analysis, acid hydrolysis, Smith degradation
- 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_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 5143
Cloutier M, Muru K, Ravicoularamin G, Gauthier C "Polysaccharides from Burkholderia species as targets for vaccine development, immunomodulation and chemical synthesis" -
Natural Product Reports 35(12) (2018) 1251-1293
Burkholderia species are a vast group of human pathogenic, phytopathogenic, and plant- or environment-associated bacteria. B. pseudomallei, B. mallei, and B. cepacia complex are the causative agents of melioidosis, glanders, and cystic fibrosis-related infections, respectively, which are fatal diseases in humans and animals. Due to their high resistance to antibiotics, high mortality rates, and increased infectivity via the respiratory tract, B. pseudomallei and B. mallei have been listed as potential bioterrorism agents by the Centers for Disease Control and Prevention. Burkholderia species are able to produce a large network of surface-exposed polysaccharides, i.e., lipopolysaccharides, capsular polysaccharides, and exopolysaccharides, which are virulence factors, immunomodulators, major biofilm components, and protective antigens, and have crucial implications in the pathogenicity of Burkholderia-associated diseases. This review provides a comprehensive and up-to-date account regarding the structural elucidation and biological activities of surface polysaccharides produced by Burkholderia species. The chemical synthesis of oligosaccharides mimicking Burkholderia polysaccharides is described in detail. Emphasis is placed on the recent research efforts toward the development of glycoconjugate vaccines against melioidosis and glanders based on synthetic or native Burkholderia oligo/polysaccharides.
lipopolysaccharides, Burkholderia, capsular polysaccharides, Oligosaccharides, glycoconjugate vaccines, antigens, exopolysaccharides, surface polysaccharide, virulence factor, Biofilm, chemical synthesis, bioterrorism
Publication DOI: 10.1039/C8NP00046HJournal NLM ID: 8502408Publisher: London: Royal Society of Chemistry
Correspondence: charles.gauthier@iaf.inrs.ca
Institutions: INRS-Institut Armand-Frappier, Universite du Quebec, 531, boul. des Prairies, Laval, Canada
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14. Compound ID: 1459
Structure type: oligomer
Aglycon: p-nitrophenyl
Trivial name: common epithope
Contained glycoepitopes: IEDB_130648,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_190606,SB_165,SB_166,SB_187,SB_195,SB_21,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 17
Blixt O, Van Die I, Norberg T, van den Eijnden DH "High-level expression of the Neisseria meningitidis lgtA gene in Escherichia coli and characterization of the encoded N-acetylglucosaminyltransferase as a useful catalyst in the synthesis of GlcNAcb1→3Gal and GalNAcb1-3Gal linkages" -
Glycobiology 9(10) (1999) 1061-1071
We have expressed the Neisseria meningitidis lgtA gene at a high level in Escherichia coli. The encoded β-N-acetylglucosaminyltransferase, referred to as LgtA, which in the bacterium is involved in the synthesis of the lacto-N-neo-tetraose structural element of the bacterial lipooligosaccharide, was obtained in an enzymatically highly active form. This glycosyltransferase appeared to be unusual in that it displays a broad acceptor specificity toward both α- and β-galactosides, whether structurally related to N- or O-protein-, or lipid-linked oligosaccharides. Product analysis by one- and two-dimensional 400 MHz 1H- and 13C NMR spectroscopy reveals that LgtA catalyzes the introduction of GlcNAc from UDP-GlcNAc in a β1→3-linkage to accepting Gal residues. The enzyme can thus be characterized as a UDP-GlcNAc:Gal α/β-R β 3-N-acetylglucosaminyltransferase. Although lactose is a highly preferred acceptor substrate the recombinant enzyme also acts efficiently on monomeric and dimeric N-acetyllactosamine revealing its potential value in the synthesis of polylactosaminoglycan structures in enzyme assisted procedures. Furthermore, LgtA shows a high donor promiscuity toward UDP-GalNAc, but not toward other UDP-sugars, and can catalyze the introduction of GalNAc in β1→3-linkage to α- or β-Gal in the acceptor structures at moderate rates. LgtA therefore shows promise to be a useful catalyst in the preparative synthesis of both GlcNAc β1→3 Gal and GalNAc β1→3 Gal linkages.
oligosaccharide, enzyme-assisted-synthesis, recombinant glycosyltransferase, glycosidic linkage, polylactosaminoglycan, recombinant glycosyltrasferase
NCBI PubMed ID: 10521543Publication DOI: 10.1093/glycob/9.10.1061Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Institutions: Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden, Department of Medical Chemistry, Vrije Universiteit, Van der Boechorstraat 7, 1081 BT Amsterdam, The Netherlands
Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, enzyme-assisted synthesis, DNA techniques, glycosyltransferase assays, kinetics assays
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15. Compound ID: 1462
|
L-gro-a-D-manHepp-(1-2)-+
|
EtN-(1--P--3)--L-gro-a-D-manHepp-(1-3)-+
|
b-D-Glcp-(1-4)-+ |
| |
a-D-GalpNAc-(1-3)-b-D-GalpNAc-(1-3)-a-D-Galp-(1-4)-b-D-Galp-(1-4)-b-D-Glcp-(1-6)-L-gro-a-D-manHepp-(1-6)-b-D-Glcp-(1-4)-L-gro-a-D-manHepp-(1-5)-a-Kdo
|
a-D-Glcp-(1-6)-+ |
Show graphically |
Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130648,IEDB_130650,IEDB_130651,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_137779,IEDB_138949,IEDB_1391961,IEDB_1391964,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_144987,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152217,IEDB_153207,IEDB_153208,IEDB_190606,IEDB_2189047,IEDB_423106,IEDB_423127,IEDB_742247,IEDB_885822,IEDB_983931,SB_165,SB_166,SB_167,SB_178,SB_187,SB_192,SB_195,SB_21,SB_31,SB_6,SB_62,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 465
St-Michael F, Vinogradov E, Li J, Cox AD "Structural analysis of the lipopolysaccharide from Pasteurella multocida genome strain Pm70 and identification of the putative lipopolysaccharide glycosyltransferases" -
Glycobiology 15(4) (2005) 323-333
Pasteurella multocida is an important multi-species veterinary pathogen. The cell surface lipopolysaccharide (LPS) is an important virulence factor and forms the basis of the serotyping scheme, although little structural information about the LPS is known. The structure of the LPS from the Pasteurella multocida genome strain Pm70 was elucidated in this study. The LPS was subjected to a variety of degradative procedures. The structures of the purified products were established by monosaccharide and methylation analyses, NMR spectroscopy and mass spectrometry. The following structure for the core oligosaccharide was determined on the basis of the combined data from these experiments, where based on the NMR data all sugars were found in pyranose ring forms. Glucose, galactose and N-acetyl-galactosamine residues were all present as D-isomers. Kdo is 2-keto-3-deoxy-octulosonic acid, L-α-D-Hep is L-glycero-D-manno-heptose, and PEtn is phosphoethanolamine. Identification of the core oligosaccharide structure enabled a search for glycosyltransferase homologues in the Pm70 genome, and revealed a clustering of the genes putatively responsible for outer core oligosaccharide biosynthesis.
Lipopolysaccharide, NMR, core oligosaccharide, mass spectrometry, nuclear magnetic resonance, Pasteurella multocida
NCBI PubMed ID: 15537789Publication DOI: 10.1093/glycob/cwi015Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: andrew.cox@nrc-cnrc.gc.ca
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, ON, Canada, K1A 0R6, Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada, K1A 0R6
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, sugar analysis, 31P NMR, ESI-MS, GLC, CE-MS
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