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1. Compound ID: 240
Structure type: polymer chemical repeating unit
Trivial name: neutral glycan
Compound class: O-polysaccharide, O-antigen, LPS
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_149136,IEDB_885822
The structure is contained in the following publication(s):
- Article ID: 60
Eserstam R, Slater C, Jansson P, Widmalm G, Rundlöf T, Wilkinson SG "Structure of the acidic microcapsular glycan from the reference strain (C.D.C. 6320-58) for Serratia marcescens serotype O14:K12" -
Carbohydrate Research 329(1) (2000) 227-232
The acidic polysaccharide from Serratia marcescens serogroup O14:K12 was analyzed by means of chemical studies and NMR spectroscopy and its repeating unit structure found to be carbohydrate sequence [see text] O-Acetyl groups are proposed to be present in non-stoichiometric amounts on O-6 on one of the hexose residues in the main chain
O-antigen, Serratia marcescens, Acidic surface glycan
NCBI PubMed ID: 11086704Publication DOI: 10.1016/S0008-6215(00)00168-3Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: pererik.jansson@kfcmail.hs.sll.se
Institutions: Clinical Research Centre, Karolinska Institute, Huddinge Hospital, NOVUM, Sweden
Methods: methylation, NMR-2D, NMR, sugar analysis
- 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: 620
Aucken HM, Wilkinson SG, Pitt TL "Re-evaluation of the serotypes of Serratia marcescens and separation into two schemes based on lipopolysaccharide (O) and capsular polysaccharide (K) antigens" -
Microbiology 144 (1998) 639-653
Chemical and serological analysis has revealed that many of the 29 O serotype reference strains of Serratia marcescens contain both neutral and acidic polysaccharides which correspond to LPS O antigens and capsular K antigens, respectively. New O and K antigen typing schemes have therefore been devised, based on the known chemical structures of the surface polysaccharides of the organism. These schemes were designed to allow the specific detection of these antigens on unknown strains using ELISAs. O antigens were detected using whole cells cultured in broth then autoclaved to remove capsular material, while K antigens were detected using formolized whole cells which had been cultured on glycerol agar to enhance capsule production. After testing with the 29 reference strains as well as 423 distinct clinical strains, it was apparent that different aspects of chemical structure were associated with different degrees of serological reactivity and the typing schemes were modified further to accommodate this. In general, the O antigen repeating unit structures were chemically simple with di- or trisaccharide backbones. Serological specificity was often provided solely by the presence or absence of an O-acetyl substituent, or a change in the linkage between two sugar residues. Five of the O serotypes in the new scheme were represented by 12 of the 29 reference strains, while three reference strains lacked O antigens altogether, resulting in the elimination of 10 of the original O types. In contrast, the K antigen repeating unit structures were more complex and chemically diverse, having at least four sugar residues. Three K types were each seen in two reference strains while 12 of the 29 reference strains were acapsular. Thus, the resulting schemes contain 19 O types and 14 K types and allow the definitive serotype identification of S. marcescens.
Lipopolysaccharide, antigen, LPS, structure, K-antigen, O-antigen, capsular polysaccharide, Serratia marcescens, Serratia, serotyping, O-serotype
NCBI PubMed ID: 9534235Journal NLM ID: 0376646Publisher: Washington, DC: Kluwer Academic/Plenum Publishers
Correspondence: haucken@phls.co.uk
Institutions: Laboratory of Hospital Infection, Central Public Health Laboratory, 61 Colindale Avenue, London NW9 5HT, UK, School of Chemistry, The University, Hull HU6 7RX, UK
Methods: NMR, SDS-PAGE, ELISA, chromatography, Quellung reaction, serum adsorption assays
- 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: 1829
Knirel YA, Shashkov AS, Dmitriev BA, Kochetkov NK, Stanislavsky ES, Mashilova GM "Antigenic polysaccharides of bacteria. 14. Structure of the O-specific polysaccharide chain of a lipopolysaccharide from Pseudomonas aeruginosa O12" -
Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 11(9) (1985) 1265-1269
The lipopolysaccharide from Pseudomonas aeruginosa O12 (Lányi classification) gave on mild acid hydrolysis an O-specific polysaccharide built of D-ribose and N-acetyl-D-galactosamine. The disaccharide structure →4)-α-GalNAcp-(1→2)-β-Ribf-(1→ for the repeating unit of the polysaccharide was established by nondestructive way involving full interpretation of its 1H- and 13C-NMR-spectra, using homonuclear and selective heteronuclear 13C[1H] double resonances.
NCBI PubMed ID: 2415135Journal NLM ID: 7804941Publisher: Moskva: Nauka
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
Methods: 13C NMR, 1H NMR
- Article ID: 1869
Knirel YA, Tanatar NV, Soldatkina MA, Zakharova IY "Antigenic polysaccharides of bacteria. 35. Structural determination of polysaccharide chains of the Pseudomonas cepacia IMV 4176 and IMV 4202 (serotype 3) lipopolysaccharides" -
Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 14(12) (1988) 1684-1689
On mild acid degradation of the Pseudomonas cepacia strain IMV 4176 lipopolysaccharide, two polysaccharides were obtained, one of which is a homopolymer of N-acetyl-D-galactosamine and the other is composed of equal amounts of N-acetyl-D-galactosamine and D-ribose. Partial hydrolysis with aqueous oxalic acid caused depolymerization of the heteropolysaccharide, and the homopolysaccharide was isolated in the individual state. On the basis of methylation and 13C NMR analysis, it was concluded that both polysaccharides are built up of disaccharide repeating units having the following structures: →4)-α-D-GalpNAc-(1→4)-β-D-GalpNAc-(1→ and →4)-α-D-GalpNAc-(1→2)-β-D-Ribf-(1→. The heteropolysaccharide from P. cepacia strain 4176 is identical by the structure of the repeating unit to the O-specific polysaccharide of P. cepacia strain IMV 4202 (serotype 3), Pseudomonas aeruginosa O12 and Serratia marcescens O14.
NCBI PubMed ID: 2472145Journal NLM ID: 7804941WWW link: http://www.rjbc.ru/arc/14/12/1684-1689.pdfPublisher: Moskva: Nauka
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
Methods: 13C NMR
- Article ID: 2010
Brigden CJ, Wilkinson SG "Lipopolysaccharide from the O14 type strain of Serratia marcescens: Structural studies of a polymeric fraction" -
Carbohydrate Research 115 (1983) 183-190
The lipopolysaccharide from Serratia marcescens C.D.C. 4444-60, the reference strain for O-serogroup 14, has been analysed. All of the phosphorus of the lipopolysaccharide appeared to be present in the lipid A region as orthophosphoric mono-and di-ester residues. Mild hydrolysis of the lipopolysaccharide with acid released orthophosphate, a 3-deoxy-2-octulosonic acid, and an unidentified related compound. The major components of the core oligosaccharide were probably d-glucose and l-glycero-d-manno-heptose; lesser components included the 3-deoxy-2-octulosonic acid, d-glycero-d-manno-heptose, and 2-amino-2-deoxyglucose. Products of high molecular weight included a polysaccharide having the disaccharide repeating-unit →4)-α-d-GalpNAc-(1 → 2)-β-d-Ribf-(1 →. The same polysaccharide was isolated from the lipopolysaccharide of a second O14 strain of S. marcescens, but was absent from a third. All three lipopolysaccharides contained polymeric material rich in glucose and mannose.
Publication DOI: 10.1016/0008-6215(83)88146-4Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Department of Chemistry, The University, Hull HU6 7RX Great Britain
Methods: 13C NMR
- Article ID: 2154
Cox AD, Wilkinson SG "Structures of the O-specific polymers from the lipopolysaccharides of the reference strains for Pseudomonas cepacia serogroups O3 and O5" -
Carbohydrate Research 195 (1989) 123-129
The putative O-specific polymers of lipopolysaccharides from two reference strains of Pseudomonas cepacia have been isolated and characterized. Both polymers have disaccharide repeating-units. Structure 1 was established for the O3 polymer, and structure 2 for the O5 polymer. Polymers with the same repeating units have been found previously as the O antigens of other bacteria. →2)-β-D-Ribf-(1→4)-α-D-GalpNAc-(1→ →4)-α-L-Rhap-(1→3)-β-D-ManpNAc-(1→.
NCBI PubMed ID: 2636041Publication DOI: 10.1016/0008-6215(89)85095-5Journal NLM ID: 0043535Publisher: Elsevier
Institutions: School of Chemistry, The University, Great Britain
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, GLC, Smith degradation
- Article ID: 2172
Oxley D, Wilkinson SG "Structural studies of acidic polymers produced by the O23 reference strain of Serratia marcescens: presence of amide-linked glutamic acid" -
Carbohydrate Research 204 (1990) 85-91
The major fraction of an acidic galactoglucomannan present in lipopolysaccharide extracts from cell walls of the O23 reference strain of Serratia marcescens has the tetrasaccharide repeating-unit shown. In a minor fraction, l-glutamic acid was amide-linked to about half of the d-glucuronic acid residues. The possible contributions of the acidic polymers and a neutral polymer produced by the organism to cross-reactions with other serogroups are discussed [structure: see text].
NCBI PubMed ID: 1980630Publication DOI: 10.1016/0008-6215(90)84023-NJournal NLM ID: 0043535Publisher: Elsevier
Institutions: School of Chemistry, The University, Hull HU6 7RX Great Britain
Methods: 13C NMR, 1H NMR
- Article ID: 2178
Kenne L, Lindberg B, Rahman MM, Mosihuzzaman M "Structural studies of the O-antigen polysaccharide of Vibrio fluvialis AA-18239" -
Carbohydrate Research 205 (1990) 440-443
No abstract available
NCBI PubMed ID: 1703458Publication DOI: 10.1016/0008-6215(90)80165-yJournal NLM ID: 0043535Publisher: Elsevier
Institutions: Department of Organic Chemistry, University of Stockholm, Sweden
Methods: 13C NMR, 1H NMR, methylation, FAB-MS, acid hydrolysis, mild acid hydrolysis, NaBH4 reduction
- 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: 5000
Hassan AA, Maldonado RF, Dos Santos SC, Di Lorenzo F, Silipo A, Coutinho CP, Cooper VS, Molinaro A, Valvano MA, Sá-Correia I "Structure of O-Antigen and Hybrid Biosynthetic Locus in Burkholderia cenocepacia Clonal Variants Recovered from a Cystic Fibrosis Patient" -
Frontiers in Microbiology 8 (2017) 1027
Burkholderia cenocepacia is an opportunistic pathogen associated with chronic lung infections and increased risk of death in patients with cystic fibrosis (CF). In this work, we investigated the lipopolysaccharide (LPS) of clinical variants of B. cenocepacia that were collected from a CF patient over a period of 3.5 years, from the onset of infection until death by necrotizing pneumonia (cepacia syndrome). We report the chemical structure of the LPS molecule of various sequential isolates and the identification of a novel hybrid O-antigen (OAg) biosynthetic cluster. The OAg repeating unit of the LPS from IST439, the initial isolate, is a [→2)-β-D-Ribf-(1→4)-α-D-GalpNAc-(1→] disaccharide, which was not previously described in B. cenocepacia. The IST439 OAg biosynthetic gene cluster contains 7 of 23 genes that are closely homologous to genes found in B. multivorans, another member of the Burkholderia cepacia complex. None of the subsequent isolates expressed OAg. Genomic sequencing of these isolates enabled the identification of mutations within the OAg cluster, but none of these mutations could be associated with the loss of OAg. This study provides support to the notion that OAg LPS modifications are an important factor in the adaptation of B. cenocepacia to chronic infection and that the heterogeneity of OAgs relates to variation within the OAg gene cluster, indicating that the gene cluster might have been assembled through multiple horizontal transmission events.
Lipopolysaccharide, O-antigen, cystic fibrosis, Burkholderia cepacia complex, chronic infection, clonal variation
NCBI PubMed ID: 28642745Publication DOI: 10.3389/fmicb.2017.01027Journal NLM ID: 101548977Publisher: Lausanne: Frontiers Research Foundation
Correspondence: sabel Sá-Correia
Institutions: Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States, Department of Chemical Sciences, University of Napoli Federico II Complesso Universitário Monte Santangelo, Napoli, Italy, The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, DNA sequencing, DNA cloning, acid hydrolysis, Western blotting, MALDI-TOF MS, composition analysis, GPC, SDS-Tricine-PAGE, function analysis of gene clusters
- 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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2. Compound ID: 257
|
-4)-a-D-Galp-(1-2)-b-D-Ribf-(1-4)-b-D-Galp-(1-4)-b-D-Glcp-(1-7)-D,D-3,9dthraltNon-onic-(2-6)-a-D-Glcp-(1-4)-b-D-GalpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_130648,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_149136,IEDB_151528,IEDB_190606,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_25,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 67
Faber EJ, Van Haaster DJ, Kamerling JP, Vliegenthart JF "Characterization of the exopolysaccharide produced by Streptococcus thermophilus 8S containing an open chain nononic acid" -
European Journal of Biochemistry 269(22) (2002) 5590-5598
The exopolysaccharide produced by Streptococcus thermophilus 8S in reconstituted skimmed milk is a heteropolysaccharide containing d-galactose, d-glucose, d-ribose, and N-acetyl-d-galactosamine in a molar ratio of 2 : 1 : 1 : 1. Furthermore, the polysaccharide contains one equivalent of a novel open chain nononic acid constituent, 3,9-dideoxy-d-threo-d-altro-nononic acid, ether-linked via C-2 to C-6 of an additional d-glucose per repeating unit. Methylation analysis and 1D/2D NMR studies (1H and 13C) performed on the native polysaccharide, and mass spectrometric and NMR analyses of the oligosaccharide obtained from the polysaccharide by de-N-acetylation followed by deamination and reduction demonstrated the 'hepta'saccharide repeating unit to be: →4)-α-D-Galp-(1→2)-β-D-Ribf-(1→4)-β-D-Galp-(1→4)-β-D-Glcp-(1→7')-Sug-(1→4)-β-D-GalpNAc-(1→ in which Sug is 6-O-(3',9'-dideoxy-d-threo-d-altro-nononic acid-2'-yl)-α-D-glucopyranose
Lactic acid bacteria, Streptococcus thermophilus, exopolysaccharide, structural analysis, nononic acid
NCBI PubMed ID: 12423358Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: j.p.kamerling@chem.uu.nl
Institutions: Bijvoet Center, Department of Bio-Organic Chemistry, Section of Glycoscience and Biocatalysis, Utrecht University, Utrecht, the Netherlands
Methods: methylation, NMR-2D, NMR, sugar analysis, MS, de-N-acetylation, deamination
- 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: 5880
De Vuyst L, De Vin F "Exopolysaccharides from Lactic Acid Bacteria" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2007) 477-519
carbohydrates, Lactic acid bacteria, exopolysaccharides, polysaccharides, glycolipids, glycoproteins, Glycomics
Publication DOI: 10.1016/B978-044451967-2/00129-XPublisher: Elsevier
Correspondence: ldvuyst@vub.ac.be
Editors: Barchi J, Kamerling H
Institutions: Department of Applied Biological Sciences and Engineering, Research Group of Industrial Microbiology and Food Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
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3. Compound ID: 258
|
a-D-Galp-(1-2)-b-D-Ribf-(1-4)-b-D-Galp-(1-4)-b-D-Glcp-(1-7)-D,D-3,9dthraltNon-onic-(2-6)-a-D-Glcp-(1-4)-D-2,5anhTal-ol |
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Structure type: oligomer
Compound class: EPS
Contained glycoepitopes: IEDB_136044,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_149136,IEDB_151528,IEDB_190606,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 67
Faber EJ, Van Haaster DJ, Kamerling JP, Vliegenthart JF "Characterization of the exopolysaccharide produced by Streptococcus thermophilus 8S containing an open chain nononic acid" -
European Journal of Biochemistry 269(22) (2002) 5590-5598
The exopolysaccharide produced by Streptococcus thermophilus 8S in reconstituted skimmed milk is a heteropolysaccharide containing d-galactose, d-glucose, d-ribose, and N-acetyl-d-galactosamine in a molar ratio of 2 : 1 : 1 : 1. Furthermore, the polysaccharide contains one equivalent of a novel open chain nononic acid constituent, 3,9-dideoxy-d-threo-d-altro-nononic acid, ether-linked via C-2 to C-6 of an additional d-glucose per repeating unit. Methylation analysis and 1D/2D NMR studies (1H and 13C) performed on the native polysaccharide, and mass spectrometric and NMR analyses of the oligosaccharide obtained from the polysaccharide by de-N-acetylation followed by deamination and reduction demonstrated the 'hepta'saccharide repeating unit to be: →4)-α-D-Galp-(1→2)-β-D-Ribf-(1→4)-β-D-Galp-(1→4)-β-D-Glcp-(1→7')-Sug-(1→4)-β-D-GalpNAc-(1→ in which Sug is 6-O-(3',9'-dideoxy-d-threo-d-altro-nononic acid-2'-yl)-α-D-glucopyranose
Lactic acid bacteria, Streptococcus thermophilus, exopolysaccharide, structural analysis, nononic acid
NCBI PubMed ID: 12423358Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: j.p.kamerling@chem.uu.nl
Institutions: Bijvoet Center, Department of Bio-Organic Chemistry, Section of Glycoscience and Biocatalysis, Utrecht University, Utrecht, the Netherlands
Methods: methylation, NMR-2D, NMR, sugar analysis, MS, de-N-acetylation, deamination
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4. Compound ID: 367
|
EtN-(1--P--3)--+
|
b-D-Galf-(1-3)-+ |
| |
-2)-a-L-Rhap-(1-2)-a-L-Rhap-(1-2)-b-D-Ribf-(1-4)-a-D-GalpA-(1-3)-a-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_133754,IEDB_136095,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_141807,IEDB_149136,IEDB_151531,IEDB_190606,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 111
Toukach FV, Shashkov AS, Katzenellenbogen E, Kocharova NA, Czarny A, Knirel YA, Romanowska E, Kochetkov NK "Structure of the O-specific polysaccharide of Hafnia alvei strain 1222 containing 2-aminoethyl phosphate" -
Carbohydrate Research 295 (1996) 117-126
The O-specific polysaccharide of H. alvei strain PCM 1222 has a branched hexasaccharide repeating unit containing D-galactose, L-rhamnose, D-ribose, D-galacturonic acid, and 2-acetamido-2-deoxy-D-glucose in the ratios 1:2:1:1:1, as well as 2-aminoethyl phosphate (xXEtNP) and O-acetyl groups in nonstoichiometric amounts. The polysaccharide was modified by carboxyl reduction, O-deacetylation, and dephosphorylation with 48% hydrofluoric acid, the last reaction being accompanied by removal of the lateral residue of β-galactofuranose. The modified polysaccharides were studied by methylation analysis and 1H and 13C NMR spectroscopy, including 2D correlation spectroscopy (COSY), H-detected 1H,13C and 1H,31P heteronuclear multiple-quantum coherence (HMQC), 1D NOE, 2D rotating-frame NOE spectroscopy (ROESY), and 2D combined total correlation spectroscopy (TOCSY) and ROESY (TORO). The following structure of the O-deacetylated polysaccharide was established: [formula: see text] In different batches of the polysaccharide, the content of xXEtNP varied from 0.35 to 0.55 and that of the O-acetyl groups from 0.05 to 0.4 per repeating unit. It was tentatively suggested that the O-acetyl group is located at position 4 of a rhamnosyl residue.
Lipopolysaccharide, LPS, structure, strain, polysaccharide, O-antigen, phosphate, O-specific, O-specific polysaccharide, Hafnia alvei, Bacterial polysaccharide, galactofuranose, 2-aminoethyl phosphate, enterobacteria, Hafnia, phosphoethanolamine, ribose
NCBI PubMed ID: 9002188Journal NLM ID: 0043535Publisher: Elsevier
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Czerska 12, 53-114 Wroclaw, Poland, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Czerska 12, 53-114 Wroclaw, Poland.
Methods: methylation, NMR-2D, NMR, dephosphorylation, carboxyl reduction, de-O-acetylation
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5. Compound ID: 452
|
-2)-a-L-Rhap-(1-2)-a-L-Rhap-(1-2)-b-D-Ribf-(1-4)-a-D-GalpA-(1-3)-a-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_133754,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_149136,IEDB_151531,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 111
Toukach FV, Shashkov AS, Katzenellenbogen E, Kocharova NA, Czarny A, Knirel YA, Romanowska E, Kochetkov NK "Structure of the O-specific polysaccharide of Hafnia alvei strain 1222 containing 2-aminoethyl phosphate" -
Carbohydrate Research 295 (1996) 117-126
The O-specific polysaccharide of H. alvei strain PCM 1222 has a branched hexasaccharide repeating unit containing D-galactose, L-rhamnose, D-ribose, D-galacturonic acid, and 2-acetamido-2-deoxy-D-glucose in the ratios 1:2:1:1:1, as well as 2-aminoethyl phosphate (xXEtNP) and O-acetyl groups in nonstoichiometric amounts. The polysaccharide was modified by carboxyl reduction, O-deacetylation, and dephosphorylation with 48% hydrofluoric acid, the last reaction being accompanied by removal of the lateral residue of β-galactofuranose. The modified polysaccharides were studied by methylation analysis and 1H and 13C NMR spectroscopy, including 2D correlation spectroscopy (COSY), H-detected 1H,13C and 1H,31P heteronuclear multiple-quantum coherence (HMQC), 1D NOE, 2D rotating-frame NOE spectroscopy (ROESY), and 2D combined total correlation spectroscopy (TOCSY) and ROESY (TORO). The following structure of the O-deacetylated polysaccharide was established: [formula: see text] In different batches of the polysaccharide, the content of xXEtNP varied from 0.35 to 0.55 and that of the O-acetyl groups from 0.05 to 0.4 per repeating unit. It was tentatively suggested that the O-acetyl group is located at position 4 of a rhamnosyl residue.
Lipopolysaccharide, LPS, structure, strain, polysaccharide, O-antigen, phosphate, O-specific, O-specific polysaccharide, Hafnia alvei, Bacterial polysaccharide, galactofuranose, 2-aminoethyl phosphate, enterobacteria, Hafnia, phosphoethanolamine, ribose
NCBI PubMed ID: 9002188Journal NLM ID: 0043535Publisher: Elsevier
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Czerska 12, 53-114 Wroclaw, Poland, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Czerska 12, 53-114 Wroclaw, Poland.
Methods: methylation, NMR-2D, NMR, dephosphorylation, carboxyl reduction, de-O-acetylation
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6. Compound ID: 592
|
D-Gro-(1--P--3)--+ b-D-Ribf-(1-6)-+
| |
-4)-b-D-Glcp-(1-2)-a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-b-D-Manp-(1-
|
Subst-(?-4)-+
Subst = N-(2-hydroxyethyl)-2-aminoethylphosphonic acid = SMILES O{1}P(CCNC{5}CO)(O)=O |
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Structure type: polymer chemical repeating unit
; 50000-150000
Compound class: CPS
Contained glycoepitopes: IEDB_130695,IEDB_136105,IEDB_137485,IEDB_142488,IEDB_144983,IEDB_146664,IEDB_149136,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_72
The structure is contained in the following publication(s):
- Article ID: 177
Vinogradov E, Egbosimba EE, Perry MB, Lam JS, Forsberg CW "Structural analysis of the carbohydrate components of the outer membrane of the lipopolysaccharide-lacking cellulolytic ruminal bacterium Fibrobacter succinogenes S85" -
European Journal of Biochemistry 268(12) (2001) 3566-3576
The polysaccharides from the outer membrane of the Gram-negative ruminal bacterium Fibrobacter succinogenes were isolated by phenol/water extraction and separated by size-exclusion chromatography in the presence of deoxycholate detergent into a lower-molecular-mass fraction designated 'glycolipid' and a high-molecular-mass 'capsular polysaccharide' fraction. Both fractions lacked typical lipopolysaccharide components including 2-keto-3-deoxyoctulosonic acid and 3-hydroxy fatty acids. Carbohydrate components of these fractions were represented by two polysaccharides and one oligosaccharide (possibly glycolipid) with the following structures: : : where HEAEP is N-(2-hydroxyethyl)-2-aminoethylphosphonic acid, found for the first time in natural compounds. The polysaccharides contained pentadecanoic acid and anteisopentadecanoic acid, possibly present as the acyl components. All constituent monosaccharides except L-rhamnose had a D- configuration. In addition to having a structural role in the outer membrane, these polysaccharides may provide protection for this lipopolysaccharide-less bacterium in the highly competitive ruminal environment, as phosphonic acids covalently linked to membrane polymers have in the past been attributed the function of stabilizing membranes in the presence of phosphatases and lipases.
NMR, structure, polysaccharide, Fibrobacter succinogenes, glycolipid
NCBI PubMed ID: 11422388Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: evguenii.vinogradov@nrc.ca
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, ON, Canada
Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR
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7. Compound ID: 595
|
Subst-(?-4)-+ b-D-Ribf-(1-6)-+
| |
-4)-b-D-Glcp-(1-2)-a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-b-D-Manp-(1-
Subst = N-(2-hydroxyethyl)-2-aminoethylphosphonic acid = SMILES O{1}P(CCNC{5}CO)(O)=O |
Show graphically |
Structure type: polymer chemical repeating unit
; 50000-150000
Compound class: CPS
Contained glycoepitopes: IEDB_136105,IEDB_137485,IEDB_142488,IEDB_144983,IEDB_146664,IEDB_149136,IEDB_152206,IEDB_225177,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_72
The structure is contained in the following publication(s):
- Article ID: 177
Vinogradov E, Egbosimba EE, Perry MB, Lam JS, Forsberg CW "Structural analysis of the carbohydrate components of the outer membrane of the lipopolysaccharide-lacking cellulolytic ruminal bacterium Fibrobacter succinogenes S85" -
European Journal of Biochemistry 268(12) (2001) 3566-3576
The polysaccharides from the outer membrane of the Gram-negative ruminal bacterium Fibrobacter succinogenes were isolated by phenol/water extraction and separated by size-exclusion chromatography in the presence of deoxycholate detergent into a lower-molecular-mass fraction designated 'glycolipid' and a high-molecular-mass 'capsular polysaccharide' fraction. Both fractions lacked typical lipopolysaccharide components including 2-keto-3-deoxyoctulosonic acid and 3-hydroxy fatty acids. Carbohydrate components of these fractions were represented by two polysaccharides and one oligosaccharide (possibly glycolipid) with the following structures: : : where HEAEP is N-(2-hydroxyethyl)-2-aminoethylphosphonic acid, found for the first time in natural compounds. The polysaccharides contained pentadecanoic acid and anteisopentadecanoic acid, possibly present as the acyl components. All constituent monosaccharides except L-rhamnose had a D- configuration. In addition to having a structural role in the outer membrane, these polysaccharides may provide protection for this lipopolysaccharide-less bacterium in the highly competitive ruminal environment, as phosphonic acids covalently linked to membrane polymers have in the past been attributed the function of stabilizing membranes in the presence of phosphatases and lipases.
NMR, structure, polysaccharide, Fibrobacter succinogenes, glycolipid
NCBI PubMed ID: 11422388Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: evguenii.vinogradov@nrc.ca
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, ON, Canada
Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR
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8. Compound ID: 659
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_141794,IEDB_149136,IEDB_151528,IEDB_190606,SB_7
The structure is contained in the following publication(s):
- Article ID: 183
Vinogradov E, Frirdich E, MacLean LL, Perry MB, Petersen BO, Duus JO, Whitfield C "Structures of lipopolysaccharides from Klebsiella pneumoniae. Eluicidation of the structure of the linkage region between core and polysaccharide O chain and identification of the residues at the non- reducing termini of the O chains" -
Journal of Biological Chemistry 277(28) (2002) 25070-25081
Deamination of LPSs from Klebsiella pneumoniae released O-chain polysaccharides together with a fragment of the core oligosaccharide. The structures of the products from serotypes O1, O2a, O2a,c, O3, O4, O5, and O12 were determined by NMR spectroscopy and chemical methods, identifying the linkage region between the O antigens and the core as well as novel residues at the non-reducing ends of the polysaccharides. All serotypes had an identical linkage between the O chain and core.
lipopolysaccharides, oligosaccharide, structure, core oligosaccharide, NMR spectroscopy, O-antigens, linkage, region, O-chain, Klebsiella pneumoniae, reducing
NCBI PubMed ID: 11986326Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: evguenii.vinogradov@nrc.ca
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, Ontario K1A 0R6, Canada, Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada, Carlsberg Laboratory, Department of Chemistry, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark
Methods: NMR-2D, NMR, serological methods, genetic methods
- Article ID: 1307
Zamze S, Martinez-Pomares L, Jones H, Taylor PR, Stillion RJ, Gordon S, Wong SY "Recognition of bacterial capsular polysaccharides and lipopolysaccharides by the macrophage mannose receptor" -
Journal of Biological Chemistry 277(44) (2002) 41613-41623
The in vitro binding of the macrophage mannose receptor to a range of different bacterial polysaccharides was investigated. The receptor was shown to bind to purified capsular polysaccharides from Streptococcus pneumoniae and to the lipopolysaccharides, but not capsular polysaccharides, from Klebsiella pneumoniae. Binding was Ca(2+)- dependent and inhibitable with d-mannose. A fusion protein of the mannose receptor containing carbohydrate recognition domains 4-7 and a full-length soluble form of the mannose receptor containing all domains external to the transmembrane region both displayed very similar binding specificities toward bacterial polysaccharides, suggesting that domains 4-7 are sufficient for recognition of these structures. Surprisingly, no direct correlation could be made between polysaccharide structure and binding to the mannose receptor, suggesting that polysaccharide conformation may play an important role in recognition. The full-length soluble form of the mannose receptor was able to bind simultaneously both polysaccharide via the carbohydrate recognition domains and sulfated oligosaccharide via the cysteine-rich domain. The possible involvement of the mannose receptor, either cell surface or soluble, in the innate and adaptive immune responses to bacterial polysaccharides is discussed
lipopolysaccharides, structure, Streptococcus pneumoniae, capsular polysaccharides, recognition, Klebsiella pneumoniae, Mannose, macrophage, receptor
NCBI PubMed ID: 12196537Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: susanne.zamze@jenner.ac.uk
Institutions: Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, United Kingdom and the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
- 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: 1817
Vasiliev VN, Zakharova IY, Sashkov AS "Structure of O-specific polysaccharides Escherichia coli strain O20ab:K84:H34 (145) and O20ac:K61:H- according to 13C NMR data" -
Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 8 (1982) 120-125
- Article ID: 3197
Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" -
FEMS Microbiology Reviews 30(3) (2006) 382-403
Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/
NMR, structure, serotype, O-antigen, Enterobacteriacea, database
NCBI PubMed ID: 16594963Publication DOI: 10.1111/j.1574-6976.2006.00016.xJournal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: andrej.weintraub@ki.se
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- 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: 5472
Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G "Structure and genetics of Escherichia coli O antigens" -
FEMS Microbiology Reviews 44(6) (2020) 655-683
Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and four (O14, O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.
structure, O antigen, Escherichia coli, gene cluster, serogroup, diversity
NCBI PubMed ID: 31778182Publication DOI: 10.1093/femsre/fuz028Journal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: G. Widmalm
; Lei Wang
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China, School of Molecular and Microbial Bioscience (G08), University of Sydney, Sydney, Australia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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9. Compound ID: 825
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_149136,IEDB_151531,IEDB_885813
The structure is contained in the following publication(s):
- Article ID: 226
Winn AM, Wilkinson SG "Structure of the O16 antigen of Stenotrophomonas maltophilia" -
Carbohydrate Research 330(2) (2001) 279-283
A polysaccharide containing D-ribose, N-acetyl-D-glucosamine, and N-acetyl-D-mannosamine was isolated from the phenol-soluble lipopolysaccharide extracted from defatted cell walls of the reference strain (560) for serogroup O16 of Stenotrophomonas maltophilia. The results of methylation analysis, chemical degradations, and NMR spectroscopy showed that the polysaccharide is based on a branched trisaccharide repeating-unit of the structure shown below. Although ribose was absent from about half of the units in the isolated polymer, the regularity and spacing of the ladder observed on SDS-PAGE of the parent lipopolysaccharide indicate that this was an artefact of the mild acid hydrolysis used to release the polymer. On the other hand, the effects of mild alkaline hydrolysis on the polymer indicated partial O-acetylation.
Lipopolysaccharide, Stenotrophomonas maltophilia, O-specific polymer
NCBI PubMed ID: 11217982Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: s.g.wilkinson@chem.hull.ac.uk
Institutions: Department of Chemistry, Faculty of Science and the Environment, University of Hull, Hull HU6 7RX, UK
Methods: methylation, NMR, chemical 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
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10. Compound ID: 1105
|
b-D-Ribf-(1-4)-a-L-Rhap-(1-3)-+
|
-4)-b-D-ManpNAc-(1-4)-b-D-Glcp-(1-4)-b-D-ManpNAc-(1-4)-a-L-Rhap-(1-P- |
Show graphically |
Structure type: polymer chemical repeating unit
Trivial name: poly(glycosyl phosphate)
Compound class: CPS
Contained glycoepitopes: IEDB_136105,IEDB_142488,IEDB_146664,IEDB_149136,IEDB_1625474,IEDB_225177,IEDB_885813,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 332
Morona JK, Morona R, Paton JC "Comparative genetics of capsular polysaccharide biosynthesis in Streptococcus pneumoniae types belonging to serogroup 19" -
Journal of Bacteriology 181(17) (1999) 5355-5364
The genetic basis for the structural diversity of capsule polysaccharide (CPS) in Streptococcus pneumoniae serogroup 19 (consisting of types 19F, 19A, 19B, and 19C) has been determined for the first time. In this study, the genetic basis for the 19A and 19C serotypes is described, and the structures of all four serogroup 19 cps loci and their flanking sequences are compared. Transformation studies show that the structural difference between the 19A and 19F CPSs is likely to be a consequence of differences between their respective polysaccharide polymerase genes (cps19aI and cps19fI). The CPS of type 19C differs from that of type 19B by the addition of glucose. We have identified a single gene difference between the two cps loci (cps19cS), which is likely to encode a glucosyl transferase. The arrangement of the genes within the cps19 loci is highly conserved, with 13 genes (cps19A to -H and cps19K to -O) common to all four serogroup 19 members. These cps genes encode functions required for the synthesis of the shared trisaccharide component of the group 19 CPS repeat unit structures. Furthermore, the genetic differences between the group 19 cps loci identified are consistent with the CPS structures of the individual serotypes. Functions have been assigned to nearly all of the cps19 gene products, based on either gene complementation or similarity to other proteins with known functions, and putative biosynthetic pathways for production of all four group 19 CPSs have been proposed.
biosynthesis, genetic, Streptococcus, Streptococcus pneumoniae, capsular polysaccharide, type, serogroup
NCBI PubMed ID: 10464207Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Correspondence: patonj@wch.sa.gov.au
Institutions: Molecular Microbiology Unit, Women's and Children's Hospital, North Adelaide, South Australia 5006, Department of Microbiology and Immunology, University of Adelaide, Adelaide, South Australia 5005
Methods: PCR, DNA sequencing, Southern blotting
- Article ID: 3365
Nikolaev AV, Botvinko IV, Ross AJ "Natural phosphoglycans containing glycosyl phosphate units: structural diversity and chemical synthesis" -
Carbohydrate Research 342(3-4) (2007) 297-344
An anomeric phosphodiester linkage formed by a glycosyl phosphate unit and a hydroxyl group of another monosaccharide is found in many glycopolymers of the outer membrane in bacteria (e.g., capsular polysaccharides and lipopolysaccharides), yeasts and protozoa. The polymers (phosphoglycans) composed of glycosyl phosphate (or oligoglycosyl phosphate) repeating units could be chemically classified as poly(glycosyl phosphates). Their importance as immunologically active components of the cell wall and/or capsule of numerous microorganisms upholds the need to develop routes for the chemical preparation of these biopolymers. In this paper, we (1) present a review of the primary structures (known to date) of natural phosphoglycans from various sources, which contain glycosyl phosphate units, and (2) discuss different approaches and recent achievements in the synthesis of glycosyl phosphosaccharides and poly(glycosyl phosphates).
synthesis, structure, polysaccharides, Phosphoglycans, Anomeric phosphodiesters
NCBI PubMed ID: 17092493Publication DOI: 10.1016/j.carres.2006.10.006Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: a.v.nikolaev@dundee.ac.uk
Institutions: College of Life Sciences, Division of Biological Chemistry and Molecular Microbiology, University of Dundee, Dundee DD1 5EH, UK.
- 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: 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: 6114
Morelli L, Lay L, Santana-Mederos D, Valdes-Balbin Y, Verez Bencomo V, van Diepen A, Hokke CH, Chiodo F, Compostella F "Glycan Array Evaluation of Synthetic Epitopes between the Capsular Polysaccharides from Streptococcus pneumoniae 19F and 19A" -
ACS Chemical Biology 16(9) (2021) 1671-1679
Vaccination represents the most effective way to prevent invasive pneumococcal diseases. The glycoconjugate vaccines licensed so far are obtained from capsular polysaccharides (CPSs) of the most virulent serotypes. Protection is largely limited to the specific vaccine serotypes, and the continuous need for broader coverage to control the outbreak of emerging serotypes is pushing the development of new vaccine candidates. Indeed, the development of efficacious vaccine formulation is complicated by the high number of bacterial serotypes with different CPSs. In this context, to simplify vaccine composition, we propose the design of new saccharide fragments containing chemical structures shared by different serotypes as cross-reactive and potentially cross-protective common antigens. In particular, we focused on Streptococcus pneumoniae (Sp) 19A and 19F. The CPS repeating units of Sp 19F and 19A are very similar and share a common structure, the disaccharide ManNAc-β-(1→4)-Glc (A-B). Herein, we describe the synthesis of a small library of compounds containing different combinations of the common 19F/19A disaccharide. The six new compounds were tested with a glycan array to evaluate their recognition by antibodies in reference group 19 antisera and factor reference antisera (reacting against 19F or 19A). The disaccharide A-B, phosphorylated at the upstream end, emerged as a hit from the glycan array screening because it is strongly recognized by the group 19 antisera and by the 19F and 19A factor antisera, with similar intensity compared with the CPSs used as controls. Our data give a strong indication that the phosphorylated disaccharide A-B can be considered a common epitope among different Sp 19 serotypes.
Streptococcus pneumoniae, capsular polysaccharides, glycan, disaccharide, glycoconjugate vaccine, vaccination, glycan epitopes
NCBI PubMed ID: 34469105Publication DOI: 10.1021/acschembio.1c00347Journal NLM ID: 101282906Publisher: Washington, DC: American Chemical Society
Correspondence: Fabrizio Chiodo < f.chiodo@amsterdamumc.nl>; Federica Compostella
Institutions: Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy, Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy, Finlay Vaccine Institute, 200 and 21 Street, 11600 Havana, Cuba, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands, Italian National Research Council (CNR), Institute of Biomolecular Chemistry (ICB), Via Campi Flegrei 34, 80078 Pozzuoli, Italy
Methods: 13C NMR, 1H NMR, NMR-2D, TLC, 31P NMR, ESI-MS, chemical synthesis, chemical methods, immunization, glycan array analysis, immobilization
Expand this compound
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11. Compound ID: 1106
|
b-D-Ribf-(1-4)-a-L-Rhap-(1-3)-+
|
-4)-b-D-ManpNAc-(1-4)-b-D-Glcp-(1-4)-b-D-ManpNAc-(1-4)-a-L-Rhap-(1-P-
|
b-D-Glcp-(1-6)-+ |
Show graphically |
Structure type: polymer chemical repeating unit
Trivial name: poly(glycosyl phosphate)
Compound class: CPS
Contained glycoepitopes: IEDB_136105,IEDB_142488,IEDB_146664,IEDB_149136,IEDB_1625474,IEDB_225177,IEDB_885813,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 332
Morona JK, Morona R, Paton JC "Comparative genetics of capsular polysaccharide biosynthesis in Streptococcus pneumoniae types belonging to serogroup 19" -
Journal of Bacteriology 181(17) (1999) 5355-5364
The genetic basis for the structural diversity of capsule polysaccharide (CPS) in Streptococcus pneumoniae serogroup 19 (consisting of types 19F, 19A, 19B, and 19C) has been determined for the first time. In this study, the genetic basis for the 19A and 19C serotypes is described, and the structures of all four serogroup 19 cps loci and their flanking sequences are compared. Transformation studies show that the structural difference between the 19A and 19F CPSs is likely to be a consequence of differences between their respective polysaccharide polymerase genes (cps19aI and cps19fI). The CPS of type 19C differs from that of type 19B by the addition of glucose. We have identified a single gene difference between the two cps loci (cps19cS), which is likely to encode a glucosyl transferase. The arrangement of the genes within the cps19 loci is highly conserved, with 13 genes (cps19A to -H and cps19K to -O) common to all four serogroup 19 members. These cps genes encode functions required for the synthesis of the shared trisaccharide component of the group 19 CPS repeat unit structures. Furthermore, the genetic differences between the group 19 cps loci identified are consistent with the CPS structures of the individual serotypes. Functions have been assigned to nearly all of the cps19 gene products, based on either gene complementation or similarity to other proteins with known functions, and putative biosynthetic pathways for production of all four group 19 CPSs have been proposed.
biosynthesis, genetic, Streptococcus, Streptococcus pneumoniae, capsular polysaccharide, type, serogroup
NCBI PubMed ID: 10464207Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Correspondence: patonj@wch.sa.gov.au
Institutions: Molecular Microbiology Unit, Women's and Children's Hospital, North Adelaide, South Australia 5006, Department of Microbiology and Immunology, University of Adelaide, Adelaide, South Australia 5005
Methods: PCR, DNA sequencing, Southern blotting
- Article ID: 3365
Nikolaev AV, Botvinko IV, Ross AJ "Natural phosphoglycans containing glycosyl phosphate units: structural diversity and chemical synthesis" -
Carbohydrate Research 342(3-4) (2007) 297-344
An anomeric phosphodiester linkage formed by a glycosyl phosphate unit and a hydroxyl group of another monosaccharide is found in many glycopolymers of the outer membrane in bacteria (e.g., capsular polysaccharides and lipopolysaccharides), yeasts and protozoa. The polymers (phosphoglycans) composed of glycosyl phosphate (or oligoglycosyl phosphate) repeating units could be chemically classified as poly(glycosyl phosphates). Their importance as immunologically active components of the cell wall and/or capsule of numerous microorganisms upholds the need to develop routes for the chemical preparation of these biopolymers. In this paper, we (1) present a review of the primary structures (known to date) of natural phosphoglycans from various sources, which contain glycosyl phosphate units, and (2) discuss different approaches and recent achievements in the synthesis of glycosyl phosphosaccharides and poly(glycosyl phosphates).
synthesis, structure, polysaccharides, Phosphoglycans, Anomeric phosphodiesters
NCBI PubMed ID: 17092493Publication DOI: 10.1016/j.carres.2006.10.006Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: a.v.nikolaev@dundee.ac.uk
Institutions: College of Life Sciences, Division of Biological Chemistry and Molecular Microbiology, University of Dundee, Dundee DD1 5EH, UK.
- 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: 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: 6114
Morelli L, Lay L, Santana-Mederos D, Valdes-Balbin Y, Verez Bencomo V, van Diepen A, Hokke CH, Chiodo F, Compostella F "Glycan Array Evaluation of Synthetic Epitopes between the Capsular Polysaccharides from Streptococcus pneumoniae 19F and 19A" -
ACS Chemical Biology 16(9) (2021) 1671-1679
Vaccination represents the most effective way to prevent invasive pneumococcal diseases. The glycoconjugate vaccines licensed so far are obtained from capsular polysaccharides (CPSs) of the most virulent serotypes. Protection is largely limited to the specific vaccine serotypes, and the continuous need for broader coverage to control the outbreak of emerging serotypes is pushing the development of new vaccine candidates. Indeed, the development of efficacious vaccine formulation is complicated by the high number of bacterial serotypes with different CPSs. In this context, to simplify vaccine composition, we propose the design of new saccharide fragments containing chemical structures shared by different serotypes as cross-reactive and potentially cross-protective common antigens. In particular, we focused on Streptococcus pneumoniae (Sp) 19A and 19F. The CPS repeating units of Sp 19F and 19A are very similar and share a common structure, the disaccharide ManNAc-β-(1→4)-Glc (A-B). Herein, we describe the synthesis of a small library of compounds containing different combinations of the common 19F/19A disaccharide. The six new compounds were tested with a glycan array to evaluate their recognition by antibodies in reference group 19 antisera and factor reference antisera (reacting against 19F or 19A). The disaccharide A-B, phosphorylated at the upstream end, emerged as a hit from the glycan array screening because it is strongly recognized by the group 19 antisera and by the 19F and 19A factor antisera, with similar intensity compared with the CPSs used as controls. Our data give a strong indication that the phosphorylated disaccharide A-B can be considered a common epitope among different Sp 19 serotypes.
Streptococcus pneumoniae, capsular polysaccharides, glycan, disaccharide, glycoconjugate vaccine, vaccination, glycan epitopes
NCBI PubMed ID: 34469105Publication DOI: 10.1021/acschembio.1c00347Journal NLM ID: 101282906Publisher: Washington, DC: American Chemical Society
Correspondence: Fabrizio Chiodo < f.chiodo@amsterdamumc.nl>; Federica Compostella
Institutions: Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy, Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy, Finlay Vaccine Institute, 200 and 21 Street, 11600 Havana, Cuba, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands, Italian National Research Council (CNR), Institute of Biomolecular Chemistry (ICB), Via Campi Flegrei 34, 80078 Pozzuoli, Italy
Methods: 13C NMR, 1H NMR, NMR-2D, TLC, 31P NMR, ESI-MS, chemical synthesis, chemical methods, immunization, glycan array analysis, immobilization
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12. Compound ID: 1182
Structure type: polymer chemical repeating unit
Compound class: CPS, O-polysaccharide
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_141794,IEDB_149136,IEDB_151528,IEDB_190606,SB_7
The structure is contained in the following publication(s):
- Article ID: 363
Rodríguez-Carvajal MA, Gonzalez L, Bernabé M, Espinosa JF, Espartero JL, Tejero-Mateo P, Gil-Serrano A, Jiménez-Barbero J "Studies on the solution conformation and dynamics of the trisaccharide repeating unit of the KPS from Sinorhizobium fredii SVQ293" -
Journal of Carbohydrate Chemistry 18(8) (1999) 891-903
The conformational behaviour of the major trisaccharide repeating unit (a-D-Galp-(1→2)-b-D-Ribf-(1→9)-a-5-O-Me-Kdnp-) of the polysaccharide from Sinorhizobium fredii SVQ293, a mutant derivative has been analysed by NMR spectroscopy and extensive molecular dynamics simulations. The results obtained indicate that the five-membered ring adopts and almost unique conformation as do the pyranose rings. The Ribj-(1→9)-a-5-O-Me-Kdnp linkage may adopt a variety of conformations while the a-D-Galp-(1→2)-b-D-Ribf- also populates an extended surface of the F/T map. Two 10 ns MD simulations using the GB/SA continuum solvent model for water and the MM3* force field provides a population distribution of conformers which satisfactorily agrees with the experimental NMR data for both the glycosidic linkages and the hydroxymethyl groups.
conformation, polysaccharide, dynamics, 3-deoxy-D-glycero-D-galacto-nonulosonic acid, Sinorhizobium, trisaccharide repeating unit
Publication DOI: 10.1080/07328309908544042Journal NLM ID: 8218151Publisher: Marcel Dekker
Institutions: Instituto Quimica Organica, CSIC, Juan de la Cierva 3, 28006 Madrid, Departamento Quimica Organica, Facultad Quimica, Univ. Senilla, 41071-Spain
Methods: NMR, MD simulations
- Article ID: 645
Gil-Serrano AM, Rodríguez-Carvajal MA, Tejero-Mateo P, Espartero JL, Thomas-Oates J, Ruiz-Sainz JE, Buendía-Clavería AM "Structural determination of a 5-O-methyl-deaminated neuraminic acid (Kdn)-containing polysaccharide isolated from Sinorhizobium fredii" -
Biochemical Journal 334(3) (1998) 585-594
The structure of a polysaccharide from Sinorhizobium fredii SVQ293, a thiamine auxotrophic mutant of S. fredii HH103, has been determined. This polysaccharide was isolated following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, collision-induced dissociation tandem MS, one-dimensional 1H and 13C NMR and two-dimensional NMR experiments, the structure was shown to consist of the following trisaccharide repeating unit →2)-α-D-Galp-(1→2)-β-D-Ribf-(1→9)-α-5-O-Me-Kdnp-(2→, in which Kdn stands for deaminated neuraminic acid; 25% of the Kdn residues are not methylated. The structure of this polysaccharide is novel and this is the first report of the presence of Kdn in a rhizobial polysaccharide, as well as being the first structure described containing 5-O-Me-Kdn. This Kdn-containing polysaccharide is not present in the wild-type strain HH103, which produces a 3-deoxy-d-manno-2-octulosonic acid (Kdo)-rich polysaccharide. We conclude that it is likely that the appearance of this new Kdn-containing polysaccharide is a consequence of the mutation.
structural, polysaccharide, determination, structural determination, acid, neuraminic acid, Sinorhizobium
NCBI PubMed ID: 9729466Publication DOI: 10.1042/bj3340585Journal NLM ID: 2984726RPublisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
Correspondence: agil@cica.es
Institutions: Departamento de Qu approximately imica Organica, Facultad de Qu approximately imica, Universidad de Sevilla, 41071-Sevilla, Spain
Methods: methylation, NMR-2D, FAB-MS, partial acid hydrolysis, NMR
- Article ID: 4050
Knirel YA, Shevelev SD, Perepelov AV "Higher aldulosonic acids: components of bacterial glycans" -
Mendeleev Communications 21(4) (2011) 173-182
Recent data on the natural occurrence, chemistry, and biochemistry of C8 and C9 aldulosonic acids (3-deoxy-d-manno-oct-2-ulosonic acid, sialic acids, N-acyl derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids, and some others) as well as on the structures and biological significance of bacterial glycans containing these higher acidic monosaccharides are summarized.
structure, Bacterial, glycan, aldulosonic acid, higher acidic monosaccharides, sialic acids
Publication DOI: 10.1016/j.mencom.2011.07.001Journal NLM ID: 9425965Publisher: Moscow: Academy of Sciences of the USSR; Cambridge,UK : Royal Society of Chemistry
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- 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
Expand this compound
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13. Compound ID: 1183
Structure type: oligomer
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_141794,IEDB_149136,IEDB_151528,IEDB_190606,SB_7
The structure is contained in the following publication(s):
- Article ID: 363
Rodríguez-Carvajal MA, Gonzalez L, Bernabé M, Espinosa JF, Espartero JL, Tejero-Mateo P, Gil-Serrano A, Jiménez-Barbero J "Studies on the solution conformation and dynamics of the trisaccharide repeating unit of the KPS from Sinorhizobium fredii SVQ293" -
Journal of Carbohydrate Chemistry 18(8) (1999) 891-903
The conformational behaviour of the major trisaccharide repeating unit (a-D-Galp-(1→2)-b-D-Ribf-(1→9)-a-5-O-Me-Kdnp-) of the polysaccharide from Sinorhizobium fredii SVQ293, a mutant derivative has been analysed by NMR spectroscopy and extensive molecular dynamics simulations. The results obtained indicate that the five-membered ring adopts and almost unique conformation as do the pyranose rings. The Ribj-(1→9)-a-5-O-Me-Kdnp linkage may adopt a variety of conformations while the a-D-Galp-(1→2)-b-D-Ribf- also populates an extended surface of the F/T map. Two 10 ns MD simulations using the GB/SA continuum solvent model for water and the MM3* force field provides a population distribution of conformers which satisfactorily agrees with the experimental NMR data for both the glycosidic linkages and the hydroxymethyl groups.
conformation, polysaccharide, dynamics, 3-deoxy-D-glycero-D-galacto-nonulosonic acid, Sinorhizobium, trisaccharide repeating unit
Publication DOI: 10.1080/07328309908544042Journal NLM ID: 8218151Publisher: Marcel Dekker
Institutions: Instituto Quimica Organica, CSIC, Juan de la Cierva 3, 28006 Madrid, Departamento Quimica Organica, Facultad Quimica, Univ. Senilla, 41071-Spain
Methods: NMR, MD simulations
Expand this compound
Collapse this compound
14. Compound ID: 1450
|
b-D-Ribf-(1-3)-+
|
-4)-a-D-GlcpA2Ac3Ac-(1-2)-a-L-Rhap4Ac-(1-3)-b-L-Rhap-(1-4)-b-L-Rhap-(1-3)-b-D-GlcpNAc6Ac-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_149136,IEDB_151531,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 461
Tao J, Feng L, Guo H, Li Y, Wang L "The O-antigen gene cluster of Shigella boydii O11 and functional identification of its wzy gene" -
FEMS Microbiology Letters 234(1) (2004) 125-132
Shigella strains are human pathogens and their identification is usually based on their O-antigens. The O-antigen gene cluster of Shigella boydii O11 was sequenced. All the expected genes for the synthesis of the O-antigen were identified on the basis of homology and genes for the biosynthesis of dTDP-l-Rhamnose, genes encoding sugar transferases, as well as genes encoding O unit flippase (wzx) and O-antigen polymerase (wzy). The identity of the putative wzy gene was confirmed by showing that a wzy deficient mutant strain of S. boydii O11 produced a semi-rough LPS phenotype. The predicted wzx gene has an opposite transcription direction to that of all of the other genes in the S. boydii O11 O-antigen gene cluster. This unusual feature for the wzx gene has only previously been reported in S. boydii O6. Further comparison revealed an evolutionary relationship between O6 and O11 O-antigen gene clusters. Adjacent-gene PCR showed that Escherichia coli O105 and S. boydii O11, which share the identical O-antigen, also have the same genes and organization for their respective O-antigen gene clusters. Three genes specific for the S. boydii O11 and E. coli O105 gene clusters were identified.
O-antigen polymerase, Molecular typing, Shigella boydii type 11
NCBI PubMed ID: 15109730Journal NLM ID: 7705721Publisher: Blackwell Publishing
Correspondence: wanglei@nankai.edu.cn
Institutions: TEDA School of biological Sciences and Biotechnology, Nankai University, 23Hong Da Street, TEDA, Tianjin, China, College of Life Sciences, Nankai University, Tianjin 300071, PR China, Tianjin State Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, China
- 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: 3197
Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" -
FEMS Microbiology Reviews 30(3) (2006) 382-403
Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/
NMR, structure, serotype, O-antigen, Enterobacteriacea, database
NCBI PubMed ID: 16594963Publication DOI: 10.1111/j.1574-6976.2006.00016.xJournal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: andrej.weintraub@ki.se
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- Article ID: 3506
Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, Reeves P, Wang L "Structure and genetics of Shigella O antigens" -
FEMS Microbiology Reviews 32(4) (2008) 627-653
This review covers the O antigens of the 46 serotypes of Shigella, but those of most Shigella flexneri are variants of one basic structure, leaving 34 Shigella distinct O antigens to review, together with their gene clusters. Several of the structures and gene clusters are reported for the first time and this is the first such group for which structures and DNA sequences have been determined for all O antigens. Shigella strains are in effect Escherichia coli with a specific mode of pathogenicity, and 18 of the 34 O antigens are also found in traditional E. coli. Three are very similar to E. coli O antigens and 13 are unique to Shigella strains. The O antigen of Shigella sonnei is quite atypical for E. coli and is thought to have transferred from Plesiomonas. The other 12 O antigens unique to Shigella strains have structures that are typical of E. coli, but there are considerably more anomalies in their gene clusters, probably reflecting recent modification of the structures. Having the complete set of structures and genes opens the way for experimental studies on the role of this diversity in pathogenicity.
structure, O antigen, Shigella, O antigen gene cluster, O antigen diversity
NCBI PubMed ID: 18422615Publication DOI: 10.1111/j.1574-6976.2008.00114.xJournal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: wanglei@nankai.edu.cn
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China.
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, serological methods, genetic methods, biochemical methods
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15. Compound ID: 1505
Structure type: polymer chemical repeating unit
; n=6-9
Compound class: CPS
Contained glycoepitopes: IEDB_114703,IEDB_146102,IEDB_146103,IEDB_149136,IEDB_591403,IEDB_910421
The structure is contained in the following publication(s):
- Article ID: 480
Fernández-Santana V, Cardoso F, Rodriguez A, Carmenate T, Peña L, Valdés Y, Hardy E, Mawas F, Heynngnezz L, Rodríguez MC, Figueroa I, Chang J, Toledo ME, Musacchio A, Hernández I, Izquierdo M, Cosme K, Roy R, Verez-Bencomo V "Antigenicity and immunogenicity of a synthetic oligosaccharide-protein conjugate vaccine against Haemophilus influenzae type b" -
Infection and Immunity 72(12) (2004) 7115-7123
Polysaccharide-protein conjugates as vaccines have proven to be very effective in preventing Haemophilus influenzae type b infections in industrialized countries. However, cost-effective technologies need to be developed for increasing the availability of anti-H. influenzae type b vaccines in countries from the developing world. Consequently, vaccine production with partially synthetic antigens is a desirable goal for many reasons. They may be rigidly controlled for purity and effectiveness while at the same time being cheap enough that they may be made universally available. We describe here the antigenicity and immunogenicity of several H. influenzae type b synthetic oligosaccharide-protein conjugates in laboratory animals. The serum of H. influenzae type b-immunized animals recognized our synthetic H. influenzae type b antigens to the same extent as the native bacterial capsular polysaccharide. Compared to the anti-H. influenzae type b vaccine employed, these synthetic versions induced similar antibody response patterns in terms of titer, specificity, and functional capacity. The further development of synthetic vaccines will meet urgent needs in the less prosperous parts of the world and remains our major goal.
Haemophilus, capsular polysaccharide, antibody response, vaccines, immunogenicity, conjugate vaccine, antigenicity, Haemophilus influenzae type b
NCBI PubMed ID: 15557635Journal NLM ID: 0246127Publisher: American Society for Microbiology
Correspondence: violeta@fq.uh.cu
Institutions: Center for the Study of Synthetic Antigens, Facultad de Quimica, Universidad de La Habana, Havana, Cuba 10400
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