Show legend Show as text

Structure type: oligomer
Trivial name: pilin glycan
Contained glycoepitopes: IEDB_114701,IEDB_150900,IEDB_167188,IEDB_174332

• Article ID: 38
  Castric P, Cassels FJ, Carlson RW "Structural characterization of the Pseudomonas aeruginosa 1244 pilin glycan" - Journal of Biological Chemistry 276(28) (2001) 26479-26485
  

  An antigenic similarity between lipopolysaccharide (LPS) and glycosylated pilin of Pseudomonas aeruginosa 1244 was noted. We purified a glycan-containing molecule from proteolytically digested pili and showed it to be composed of three sugars and serine. This glycan competed with pure pili and LPS for reaction with an LPS-specific monoclonal antibody, which also inhibited twitching motility by P. aeruginosa bearing glycosylated pili. One-dimensional NMR analysis of the glycan indicated the sugars to be 5N β OHC(4)7NfmPse, Xyl, and FucNAc. The complete proton assignments of these sugars as well as the serine residue were determined by COSY and TOCSY. Electrospray ionization mass spectrometry (MS) determined the mass of this molecule to be 771.5. The ROESY NMR spectrum, tandem MS/MS analysis, and methylation analysis provided information on linkage and the sequence of oligosaccharide components. These data indicated that the molecule had the following structure: α-5N β OHC(4)7NFmPse-(2→4)β-Xyl-(1→3)-β-FucNAc-(1→3)-β-Ser

  structural, characterization, Pseudomonas, Pseudomonas aeruginosa, glycan, pilin, pseudaminic acid

  NCBI PubMed ID: 11342554
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: castric@duq.edu
  Institutions: Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
  Methods: 1H NMR, GLC-MS, NMR-2D, sugar analysis, ESI-MS, Western blotting, amino acid analysis, MS/MS
  
   
  
  Pseudomonas aeruginosa 1244
  CSDB ID 1697 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: CPS, K-antigen

• Article ID: 364
  Rodríguez-Carvajal MA, Bernabé M, Espartero JL, Tejero-Mateo P, Gil-Serrano A, Jiménez-Barbero J "Studies on the solution conformation and dynamics of a polysaccharide from Sinorhizobium fredii HH103 and its monosaccharide repeating unit" - Journal of Molecular Graphics and Modelling 18(2) (2000) 135-142
  

  The conformational behavior of the homopolysaccharide isolated from Sinorhizobium fredii HH103 and its monosaccharide repeating unit (5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulosonic acid) was analyzed by nuclear magnetic resonance (NMR) spectroscopy and extensive molecular dynamics simulations (MD). The results indicate that the glycosidic linkages and lateral cheins may adopy a variety of conformations. MD simulations using the generalized Born solvent-accessible surface area (GB/SA) continuum solvent model for water and the MM3* force field provide a population distribution of conformers that satisfactorily agrees with the experimental NMR data for the torsional degrees of freedom of the molecule.

  NMR, K-antigen, polysaccharide, molecular dynamics, pseudaminic acid

  NCBI PubMed ID: 10994517
  Journal NLM ID: 9716237
  Publisher: New York, NY: Elsevier
  Correspondence: iqoj101@iqoug.csic.es
  Institutions: Departamento Quimica Organica, Facultad Quimica, University of Sevilla, Sevilla, Spain, Instituto Quimica Organica, CSIC, Madrid, Spain, Dpto. Quimica Organica y Farmaceutica, Facultad Farmacia, University of Sevilla, Sevilla, Spain
  Methods: NMR, MD simulations
  
   
  
  Sinorhizobium fredii HH103
  CSDB ID 8063 (all data & tools)
• Article ID: 5748
  Chidwick HS, Fascione MA "Mechanistic and structural studies into the biosynthesis of the bacterial sugar pseudaminic acid (Pse5Ac7Ac)" - Organic and Biomolecular Chemistry 18(5) (2020) 799-809
  

  The non-mammalian nonulosonic acid sugar pseudaminic acid (Pse) is present on the surface of a number of human pathogens including Campylobacter jejuni and Helicobacter pylori and other bacteria such as multidrug resistant Acinetobacter baumannii. It is likely important for evasion of the host immune sysyem, and also plays a role in bacterial motility through flagellin glycosylation. Herein we review the mechanistic and structural characterisation of the enzymes responsible for the biosynthesis of the Pse parent structure, Pse5Ac7Ac in bacteria.

  biosynthesis, structure, Acinetobacter baumannii, Campylobacter jejuni, pseudaminic acid, nonulosonic acid, Helicobacter pylori, structural studies, Enzymes, glycosylation, immune, Flagellin

  NCBI PubMed ID: 31913385
  Publication DOI: 10.1039/c9ob02433f
  Journal NLM ID: 101154995
  Publisher: The Royal Society of Chemistry
  Correspondence: martin.fascione@york.ac.uk
  Institutions: Department of Chemistry, University of York, York, YO10 5DD, UK
  
   
  
  Sinorhizobium fredii
  CSDB ID 3327 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: K-antigen

• Article ID: 646
  Gil-Serrano AM, Rodríguez-Carvajal MA, Tejero-Mateo P, Espartero JL, Menendez M, Corzo J, Ruiz-Sainz JE, Buendía-Clavería AM "Structural determination of a 5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulosonic acid-containing homopolysaccharide isolated from Sinorhizobium fredii HH103" - Biochemical Journal 342(3) (1999) 527-535
  

  The structure of a polysaccharide from Sinorhizobium fredii HH103 has been determined. This polysaccharide was isolated by following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, matrix-assisted laser desorption ionization MS, electron-impact high-resolution MS, one-dimensional (1)H-NMR and (13)C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a homopolymer of a 3:1 mixture of 5-acetamido-3,5,7, 9-tetradeoxy-7-[(R)- and (S)-3-hydroxybutyramido]-l-glycero-l-manno-nonulosonic acid. The sugar residues are attached via a glycosidic linkage to the OH group of the 3-hydroxybutyramido substituent and thus the monomers are linked via both glycosidic and amidic linkages. In contrast with the Sinorhizobium K-antigens previously reported, which are composed of a disaccharide repeating unit, the K-antigen polysacharide of S. fredii HH103 is a homopolysaccharide.

  structural, K-antigen, determination, structural determination, acid, capsular polysaccharide, pseudaminic acid, 5, 7-diamino-3, 7, Sinorhizobium, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 10477263
  Journal NLM ID: 2984726R
  Publisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
  Correspondence: agil@cica.es
  Institutions: Departamento de Quimica Organica, Facultad de Quimica, Universidad de Sevilla, 41071 Sevilla, Spain, Departamento de Quimica Organica y Farmaceutica, Facultad de Farmacia, Universidad de Sevilla, 41071 Sevilla, Spain, Departamento de Bioquimica y Biologia Molecular, Facultad de Biologia, Universidad de La Laguna, 38206 Tenerife, Spain, Departamento de Microbiologia, Facultad de Biologia, Universidad de Sevilla, 41080 Sevilla, Spain.
  Methods: methylation, NMR-2D, FAB-MS, NMR, MALDI-MS
  
   
  
  Sinorhizobium fredii HH103
  CSDB ID 420 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: K-antigen

• Article ID: 646
  Gil-Serrano AM, Rodríguez-Carvajal MA, Tejero-Mateo P, Espartero JL, Menendez M, Corzo J, Ruiz-Sainz JE, Buendía-Clavería AM "Structural determination of a 5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulosonic acid-containing homopolysaccharide isolated from Sinorhizobium fredii HH103" - Biochemical Journal 342(3) (1999) 527-535
  

  The structure of a polysaccharide from Sinorhizobium fredii HH103 has been determined. This polysaccharide was isolated by following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, matrix-assisted laser desorption ionization MS, electron-impact high-resolution MS, one-dimensional (1)H-NMR and (13)C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a homopolymer of a 3:1 mixture of 5-acetamido-3,5,7, 9-tetradeoxy-7-[(R)- and (S)-3-hydroxybutyramido]-l-glycero-l-manno-nonulosonic acid. The sugar residues are attached via a glycosidic linkage to the OH group of the 3-hydroxybutyramido substituent and thus the monomers are linked via both glycosidic and amidic linkages. In contrast with the Sinorhizobium K-antigens previously reported, which are composed of a disaccharide repeating unit, the K-antigen polysacharide of S. fredii HH103 is a homopolysaccharide.

  structural, K-antigen, determination, structural determination, acid, capsular polysaccharide, pseudaminic acid, 5, 7-diamino-3, 7, Sinorhizobium, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 10477263
  Journal NLM ID: 2984726R
  Publisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
  Correspondence: agil@cica.es
  Institutions: Departamento de Quimica Organica, Facultad de Quimica, Universidad de Sevilla, 41071 Sevilla, Spain, Departamento de Quimica Organica y Farmaceutica, Facultad de Farmacia, Universidad de Sevilla, 41071 Sevilla, Spain, Departamento de Bioquimica y Biologia Molecular, Facultad de Biologia, Universidad de La Laguna, 38206 Tenerife, Spain, Departamento de Microbiologia, Facultad de Biologia, Universidad de Sevilla, 41080 Sevilla, Spain.
  Methods: methylation, NMR-2D, FAB-MS, NMR, MALDI-MS
  
   
  
  Sinorhizobium fredii HH103
  CSDB ID 554 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137473,IEDB_140630

• Article ID: 1025
  Muldoon J, Shashkov AS, Senchenkova SN, Tomshich SV, Komandrova NA, Romanenko LA, Knirel YA, Savage AV "Structure of an acidic polysaccharide from a marine bacterium Pseudoalteromonas distincta KMM 638 containing 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid" - Carbohydrate Research 330 (2001) 231-239
  

  An acidic polysaccharide was obtained from the lipopolysaccharide of Pseudoalteromonas distincta strain KMM 638, isolated from a marine sponge, and found to contain D-GlcA, D-GalNAc, 2-acetamido-2,6-dideoxy-D-glucose (D-QuiNAc) and two unusual acidic amino sugars: 2-acetamido-2-deoxy-D-galacturonic acid (D-GalNAcA) and 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid (Pse5Ac7Fo, a derivative of pseudaminic acid). Oligosaccharides were derived from the polysaccharide by partial acid hydrolysis and mild alkaline degradation and characterised by electrospray ionisation (ESI) MS and 1H and 13C NMR spectroscopy. Based on these data and NMR spectroscopic studies of the initial and O-deacetylated polysaccharides, including quaternary carbon detection, 2D COSY, TOCSY, ROESY, H-detected 1H,13C HMQC and HMBC experiments, the following structure of the branched pentasaccharide repeating unit was established: [structure: see text].

  structure, strain, polysaccharide, acidic, acidic polysaccharide, acid, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, 5, 7-diamino-3, 7, marine, Pseudoalteromonas, 2-amino-2-deoxygalacturonic acid, 9-teradeoxy-L-glycero-L-manno-nonulosonic acid

  NCBI PubMed ID: 11217976
  Publication DOI: 10.1016/S0008-6215(00)00280-9
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: angela.savage@nuigalway.ie
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Chemistry, National University of Ireland, Galway, Ireland, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladi6ostok 690022, Russia
  Methods: NMR-2D, partial acid hydrolysis, NMR, ESI-MS, de-O-acetylation
  
   
  
  Pseudoalteromonas distincta KMM 638
  CSDB ID 3719 (all data & tools)
• Article ID: 4435
  Nazarenko EL, Komandrova NA, Gorshkova RP, Tomshich SV, Zubkov VA, Kilcoyne M, Savage AV "Structures of polysaccharides and oligosaccharides of some Gram-negative marine Proteobacteria" - Carbohydrate Research 338(23) (2003) 2449-2457
  

  The chemical structures of polysaccharides and LPS core oligosaccharides, isolated from various Gram-negative marine bacteria from the genera Pseudoalteromonas and Shewanella belonging to the Alteromonadaceae family and gamma-subclass of Proteobacteria, are reviewed. The polysaccharides are distinguished by the acidic character (e.g., due to the presence of hexuronic and aldulosonic acids and their derivatives) and the occurrence of unusual sugars, including N-acyl derivatives of 6-deoxyamino sugars, such as N-acetyl-D-quinovosamine, N-acetyl-L-fucosamine and N-acetyl-6-deoxy-L-talosamine, and higher sugars like 2,6-dideoxy-2-acetamido-4-C-(3'-carboxamide-2',2'-dihydroxypropyl)-D-galac topyranose (shewanellose). Many constituent sugars have various uncommon non-sugar substituents, such as alanine, formic, lactic and hydroxybutyric acids, sulfate, phosphate, and 2-aminopropane-1,3-diol.

  Lipopolysaccharide, oligosaccharide structure, O-antigen, polysaccharide structure, Shewanella, Pseudoalteromonas, Proteobacteria

  NCBI PubMed ID: 14670708
  Publication DOI: 10.1016/j.carres.2003.06.004
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: A.V. Savage
  Institutions: Department of Chemistry, National University of Ireland, Galway, Ireland, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russian Federation
  
   
  
  Pseudoalteromonas distincta KMM 638
  CSDB ID 28824 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137473,IEDB_140630

• Article ID: 1025
  Muldoon J, Shashkov AS, Senchenkova SN, Tomshich SV, Komandrova NA, Romanenko LA, Knirel YA, Savage AV "Structure of an acidic polysaccharide from a marine bacterium Pseudoalteromonas distincta KMM 638 containing 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid" - Carbohydrate Research 330 (2001) 231-239
  

  An acidic polysaccharide was obtained from the lipopolysaccharide of Pseudoalteromonas distincta strain KMM 638, isolated from a marine sponge, and found to contain D-GlcA, D-GalNAc, 2-acetamido-2,6-dideoxy-D-glucose (D-QuiNAc) and two unusual acidic amino sugars: 2-acetamido-2-deoxy-D-galacturonic acid (D-GalNAcA) and 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid (Pse5Ac7Fo, a derivative of pseudaminic acid). Oligosaccharides were derived from the polysaccharide by partial acid hydrolysis and mild alkaline degradation and characterised by electrospray ionisation (ESI) MS and 1H and 13C NMR spectroscopy. Based on these data and NMR spectroscopic studies of the initial and O-deacetylated polysaccharides, including quaternary carbon detection, 2D COSY, TOCSY, ROESY, H-detected 1H,13C HMQC and HMBC experiments, the following structure of the branched pentasaccharide repeating unit was established: [structure: see text].

  structure, strain, polysaccharide, acidic, acidic polysaccharide, acid, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, 5, 7-diamino-3, 7, marine, Pseudoalteromonas, 2-amino-2-deoxygalacturonic acid, 9-teradeoxy-L-glycero-L-manno-nonulosonic acid

  NCBI PubMed ID: 11217976
  Publication DOI: 10.1016/S0008-6215(00)00280-9
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: angela.savage@nuigalway.ie
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Chemistry, National University of Ireland, Galway, Ireland, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladi6ostok 690022, Russia
  Methods: NMR-2D, partial acid hydrolysis, NMR, ESI-MS, de-O-acetylation
  
   
  
  Pseudoalteromonas distincta KMM 638
  CSDB ID 3893 (all data & tools)

Show legend Show as text

Structure type: monomer
Aglycon: FLaA and FLaB proteins
Contained glycoepitopes: IEDB_838988

• Article ID: 1178
  Schirm M, Soo EC, Aubry AJ, Austin J, Thibault P, Logan SM "Structural, genetic and functional characterization of the flagellin glycosylation process in Helicobacter pylori" - Molecular Microbiology 48(6) (2003) 1579-1592
  

  Mass spectrometry analyses of the complex polar flagella from Helicobacter pylori demonstrated that both FlaA and FlaB proteins are post-translationally modified with pseudaminic acid (Pse5Ac7Ac, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno -n o n-ulosonic acid). Unlike Campylobacter, flagellar glycosylation in Helicobacter displays little heterogeneity in isoform or glycoform distribution, although all glycosylation sites are located in the central core region of the protein monomer in a manner similar to that found in Campylobacter. Bioinformatic analysis revealed five genes (HP0840, HP0178, HP0326A, HP0326B, HP0114) homologous to other prokaryote genes previously reported to be involved in motility, flagellar glycosylation or polysaccharide biosynthesis. Insertional mutagenesis of four of these homologues in Helicobacter (HP0178, HP0326A, HP0326B, HP0114) resulted in a non-motile phenotype, no structural flagella filament and only minor amounts of flagellin protein detectable by Western immunoblot. However, mRNA levels for the flagellin structural genes remained unaffected by each mutation. In view of the combined bioinformatic and structural evidence indicating a role for these gene products in glycan biosynthesis, subsequent investigations focused on the functional characterization of the respective gene products. A novel approach was devised to identify biosynthetic sugar nucleotide precursors from intracellular metabolic pools of parent and isogenic mutants using capillary electrophoresis-electrospray mass spectrometry (CE-ESMS) and precursor ion scanning. HP0326A, HP0326B and the HP0178 gene products are directly involved in the biosynthesis of the nucleotide-activated form of Pse, CMP-Pse. Mass spectral analyses of the cytosolic extract from the HP0326A and HP0326B isogenic mutants revealed the accumulation of a mono- and a diacetamido trideoxyhexose UDP sugar nucleotide precursor

  biosynthesis, genetic, core, Bacterial Proteins, biosynthetic, chemistry, functional, gene, genetics, growth & development, human, metabolism, microbiology, phenotype, role, Sequence Analysis, DNA, structural, characterization, polysaccharide, analysis, ion, form, acid, animal, Campylobacter, complex, Female, level, mice, Molecular Sequence Data, protein, spectrometry, mutant, mutants, glycan, pseudaminic acid, sugar, core region, region, mass spectrometry, precursor, modified, Helicobacter pylori, mutation, intracellular, polar, site, glycosylation, Helicobacter, proteins, mutagenesis, isogenic, distribution, amino acid sequence, electrophoresis, heterogeneity, Mass, Electrospray Ionization, physiology, approach, accumulation, polysaccharide biosynthesis, homologous, extract, Capillary, flagella, Flagellin, mRNA, Stomach, sugar nucleotide

  NCBI PubMed ID: 12791140
  Journal NLM ID: 8712028
  Publisher: Blackwell Publishing
  Correspondence: susan.logan@nrc.ca
  Institutions: University of Montreal, Department of Chemistry, Canada
  
   
  
  Helicobacter pylori
  CSDB ID 4618 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: pilin
Trivial name: O-linked glycoprotein
Compound class: O-glycoprotein
Contained glycoepitopes: IEDB_114701,IEDB_167188,IEDB_174332

• Article ID: 1405
  Comer JE, Marshall MA, Blanch VJ, Deal CD, Castric P "Identification of the Pseudomonas aeruginosa 1244 pilin glycosylation site" - Infection and Immunity 70(6) (2002) 2837-2845
  

  Pseudomonas, Pseudomonas aeruginosa, pilin, pseudaminic acid, identification, site, glycosylation

  Journal NLM ID: 0246127
  Publisher: American Society for Microbiology
  Correspondence: castric@dug.edu
  Institutions: Department of Biological Sciences, Duguesne University, Pittsburgh, USA
  
   
  
  Pseudomonas aeruginosa 1244
  CSDB ID 6538 (all data & tools)
• Article ID: 4537
  Iwashkiw JA, Vozza NF, Kinsella RL, Feldman MF "Pour some sugar on it: the expanding world of bacterial protein O-linked glycosylation" - Molecular Microbiology 89(1) (2013) 14-28
  

  Protein glycosylation was once considered as an eccentricity of a few bacteria. However in the recent years multiple O-glycosylation mechanisms have been identified in bacterial species from the most diverse genera, including various important human pathogens. This review focuses on summarizing the structural diversity, the various pathways and the physiological roles of this post-translational protein modification. We propose a classification of O-glycosylation based on the requirement of an oligosaccharyltransferase (OTase). OTase-dependent glycosylation utilizes an oligosaccharide synthesized on a lipid carrier that is transferred to proteins en bloc by an OTase. Multiple proteins, including the pilins, are glycosylated using this mechanism. OTase-independent glycosylation refers to the pathway in which glycosyltransferases sequentially add monosaccharides onto the target proteins. This pathway is employed for glycosylation of flagella and autotransporters. Both systems play key roles in pathogenesis. Exploiting glycosylation machineries it is now possible to generate glycoconjugates made of different proteins attached to polysaccharides derived from LPS or capsule biosynthesis. These recombinant glycoproteins can be exploited for vaccines and diagnostics of bacterial infections. Furthermore, O-glycosylation systems are promising targets for antibiotic development. Technological advances in MS and NMR will facilitate the discovery of novel glycosylation systems. Likely, the O-glycosylation pathways we currently know constitute just the tip of the iceberg of a still largely uncharacterized bacterial glycosylation world.

  biosynthesis, glycoconjugates, bacteria, glycosyltransferases, capsule, glycoproteins, flagella, Glycomics, O-glycosylation

  NCBI PubMed ID: 23679002
  Publication DOI: 10.1111/mmi.12265
  Journal NLM ID: 8712028
  Publisher: Blackwell Publishing
  Correspondence: mfeldman@ualberta.ca
  Institutions: Alberta Glycomics Centre, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
  
   
  
  Pseudomonas aeruginosa 1244
  CSDB ID 29574 (all data & tools)
• Article ID: 6301
  Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" - Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
  

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

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

  NCBI PubMed ID: 35750381
  Publication DOI: 10.1016/S1875-5364(22)60177-8
  Journal NLM ID: 101504416
  Publisher: Beijing: Science Press; Elsevier
  Correspondence: J. Yin
  Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
  
   
  
  Pseudomonas aeruginosa 1244
  CSDB ID 21180 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: CPS

• Article ID: 1470
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Sinorhizobium fredii HH103
  CSDB ID 2827 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_114701,IEDB_167188,IEDB_174332

• Article ID: 1470
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Pseudomonas aeruginosa O7a,7b,7c
  CSDB ID 31920 (all data & tools)
• Article ID: 3207
  Knirel YA, Bystrova OV, Kocharova NA, Zähringer U, Pier GB "Conserved and variable structural features of the Pseudomonas aeruginosa lipopolysaccharide" - Journal of Endotoxin Research 12(6) (2006) 324-336
  

  The review is devoted to recent progress in the structural elucidation of the lipopolysaccharide of the bacterium Pseudomonas aeruginosa, including O-antigen biological repeats, core oligosaccharide, and lipid A. Data on biosynthesis, genetics and serology of the lipopolysaccharide isolated from various P. aeruginosa O-serogroups are discussed in relation to the chemical structures.

  O-antigen, Pseudomonas aeruginosa, lipid A, core oligosaccharide, lipopolysaccharide structure, serologic activity

  NCBI PubMed ID: 17254386
  Publication DOI: 10.1179/096805106X118906
  Journal NLM ID: 9433350
  Publisher: Maney Publishing
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
  Methods: NMR, chemical methods, MS, serological methods, genetic methods
  
   
  
  Pseudomonas aeruginosa O7 O7a,7b,7c
  CSDB ID 20571 (all data & tools)
• Article ID: 3711
  King JD, Kocincova D, Westman EL, Lam JS "Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa" - Innate Immunity 15(5) (2009) 261-312
  

  Pseudomonas aeruginosa causes serious nosocomial infections, and an important virulence factor produced by this organism is lipopolysaccharide (LPS). This review summarizes knowledge about biosynthesis of all three structural domains of LPS - lipid A, core oligosaccharide, and O polysaccharides. In addition, based on similarities with other bacterial species, this review proposes new hypothetical pathways for unstudied steps in the biosynthesis of P. aeruginosa LPS. Lipid A biosynthesis is discussed in relation to Escherichia coli and Salmonella, and the biosyntheses of core sugar precursors and core oligosaccharide are summarised. Pseudomonas aeruginosa attaches a Common Polysaccharide Antigen and O-Specific Antigen polysaccharides to lipid A-core. Both forms of O polysaccharide are discussed with respect to their independent synthesis mechanisms. Recent advances in understanding O-polysaccharide biosynthesis since the last major review on this subject, published nearly a decade ago, are highlighted. Since P. aeruginosa O polysaccharides contain unusual sugars, sugar-nucleotide biosynthesis pathways are reviewed in detail. Knowledge derived from detailed studies in the O5, O6 and O11 serotypes is applied to predict biosynthesis pathways of sugars in poorly-studied serotypes, especially O1, O4, and O13/O14. Although further work is required, a full understanding of LPS biosynthesis in P. aeruginosa is almost within reach.

  Lipopolysaccharide, core, O-antigen, Pseudomonas aeruginosa, lipid A

  NCBI PubMed ID: 19710102
  Publication DOI: 10.1177/1753425909106436
  Journal NLM ID: 101469670
  Publisher: Sage Publications
  Correspondence: jlam@uoguelph.ca
  Institutions: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
  
   
  
  Pseudomonas aeruginosa O7
  CSDB ID 24035 (all data & tools)
• Article ID: 3873
  Knirel YA, Bystrova OV, Kocharova NA, Zähringer U, Pier GB "Corrigendum: Conserved and variable structural features in the lipopolysaccharide of Pseudomonas aeruginosa" - Innate Immunity 16(4) (2010) 274
  

  The review is devoted to recent progress in the structural elucidation of the lipopolysaccharide of the bacterium Pseudomonas aeruginosa, including O-antigen biological repeats, core oligosaccharide, and lipid A. Data on biosynthesis, genetics and serology of the lipopolysaccharide isolated from various P. aeruginosa O-serogroups are discussed in relation to the chemical structures.

  Lipopolysaccharide, structure, Pseudomonas aeruginosa, core oligosaccharide, variable

  Publication DOI: 10.1177/1753425910369459
  Journal NLM ID: 101469670
  Publisher: Sage Publications
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Pseudomonas aeruginosa O7a,7b,7c, Pseudomonas aeruginosa 7
  CSDB ID 25304 (all data & tools)
• Article ID: 4062
  Lam JS, Taylor VL, Islam ST, Hao Y, Kocincova D "Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide" - Frontiers in Microbiology 2 (2011) 118
  

  Lipopolysccharide (LPS) is an integral component of the Pseudomonas aeruginosa cell envelope, occupying the outer leaflet of the outer membrane in this Gram-negative opportunistic pathogen. It is important for bacterium-host interactions and has been shown to be a major virulence factor for this organism. Structurally, P. aeruginosa LPS is composed of three domains, namely, lipid A, core oligosaccharide, and the distal O antigen (O-Ag). Most P. aeruginosa strains produce two distinct forms of O-Ag, one a homopolymer of D-rhamnose that is a common polysaccharide antigen (CPA, formerly termed A band), and the other a heteropolymer of three to five distinct (and often unique dideoxy) sugars in its repeat units, known as O-specific antigen (OSA, formerly termed B band). Compositional differences in the O units among the OSA from different strains form the basis of the International Antigenic Typing Scheme for classification via serotyping of different strains of P. aeruginosa. The focus of this review is to provide state-of-the-art knowledge on the genetic and resultant functional diversity of LPS produced by P. aeruginosa. The underlying factors contributing to this diversity will be thoroughly discussed and presented in the context of its contributions to host-pathogen interactions and the control/prevention of infection.

  Lipopolysaccharide, biosynthesis, virulence, serotyping, bacteriophage, motility, seroconversion, nucleotide sugars

  NCBI PubMed ID: 21687428
  Publication DOI: 10.3389/fmicb.2011.00118
  Journal NLM ID: 101548977
  Publisher: Lausanne: Frontiers Research Foundation
  Correspondence: jlam@uoguelph.ca
  Institutions: Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
  
   
  
  Pseudomonas aeruginosa O7
  CSDB ID 26868 (all data & tools)
• Article ID: 4684
  Islam ST, Lam JS "Synthesis of bacterial polysaccharides via the Wzx/Wzy-dependent pathway" - Canadian Journal of Microbiology 60(11) (2014) 697-716
  

  The surfaces of bacteria mediate a multitude of functions in the environment and in an infected host, including adhesion to both biotic and abiotic substrata, motility, immune system interaction and (or) activation, biofilm formation, and cell-cell communication, with many of these features directly influenced by cell-surface glycans. In both Gram-negative and Gram-positive bacteria, the majority of cell-surface polysaccharides are produced via the Wzx/Wzy-dependent assembly pathway; these glycans include heteropolymeric O-antigen, enterobacterial common antigen, exopolysaccharide, spore coat, and capsule in diverse bacteria. The key components of this assembly pathway are the integral inner membrane Wzx flippase, Wzy polymerase, and Wzz chain-length regulator proteins, which until recently have resisted detailed structural and functional characterization. In this review, we have provided a comprehensive synthesis of the latest structural and mechanistic data for each protein, as well as an examination of substrate specificity for each assembly step and complex formation between the constituent proteins. To complement the unprecedented explosion of genomic-sequencing data for bacteria, we have also highlighted both classical and state-of-the-art methods by which encoded Wzx, Wzy, and Wzz proteins can be reliably identified and annotated, using the model Gram-negative bacterium Pseudomonas aeruginosa as an example data set. Lastly, we outline future avenues of research, with the aim of stimulating researchers to take the next steps in investigating the function of, and interplay between, the constituents of this widespread assembly scheme.

  Membrane Proteins, lipopolysaccharide (LPS), Wzx flippase, Wzy polymerase, Wzz polysaccharide copolymerase

  NCBI PubMed ID: 25358682
  Publication DOI: 10.1139/cjm-2014-0595
  Journal NLM ID: 0372707
  Publisher: National Research Council of Canada
  Correspondence: sislam@imm.cnrs.fr; jlam@uoguelph.ca
  Institutions: Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
  Methods: SDS-PAGE, genetic methods, cloning
  
   
  
  Pseudomonas aeruginosa O7
  CSDB ID 30281 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_114701,IEDB_167188,IEDB_174332

• Article ID: 1470
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Pseudomonas aeruginosa O7a,7b,7d
  CSDB ID 31921 (all data & tools)
• Article ID: 1838
  Knirel YA, Kocharova NA, Shashkov AS, Dmitriev BA, Kochetkov NK, Stanislavsky ES, Mashilova GM "Antigenic polysaccharides of bacteria. 18. Structure of O-specific polysaccharide chains of Pseudomonas aeruginosa O5 (Lanyi) lipopolysaccharides" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 12 (1986) 1384-1390
  

  Polysaccharide chains of P. aeruginosa O5a, b, c, O5a, b, d and O5a, d (Lányi classification) lipopolysaccharides contain D-xylose, N-acetyl-D-fucosamine (FucNAc) and a derivative of 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic acid (pseudaminic acid, PseN2) carrying acetyl or (R)-3-hydroxybutyryl (Hb) and formyl (Fm) groups as N-acyl substituents. Degradation of the lipopolysaccharides with dilute acetic acid caused depolymerisation of the polysaccharide chains as a result of cleavage of glycosidic linkage of pseudaminic acid to give trisaccharides representing chemical repeating units of the polysaccharides. Basing on analysis of the trisaccharides using 1H and 13C NMR spectroscopy and mass-spectrometry, the following structures of the polysaccharide chains were established: (Formula: see text). O5a, d polysaccharide is identical to P. aeruginosa immunotype 6 O-specific polysaccharide.

  NCBI PubMed ID: 2434100
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
  Methods: 13C NMR
  
   
  
  Pseudomonas aeruginosa O5a,b,d
  CSDB ID 110557 (all data & tools)
• Article ID: 2403
  Knirel YA, Kocharova NA, Shashkov AS, Dmitriev BA, Kochetkov NK, Stanislavsky ES, Mashilova GM "Somatic antigens of Pseudomonas aeruginosa. The structure of O-specific polysaccharide chains of the lipopolysaccharides from P.aeruginosa O5 (Lányi) and immunotype 6 (Fisher)" - European Journal of Biochemistry 163 (1987) 639-652
  

  Lipopolysaccharides were isolated from dry bacterial cells of Pseudomonas aeruginosa O5a,b,c, O5a,b,d, O5a,d (Lányi classification) and immunotype 6 (Fisher classification) by the Westphal procedure. Their polysaccharide chains were built up of trisaccharide repeating units containing D-xylose, 2-acetamido-2,6-dideoxy-D-galactose and a new sialic acid-like sugar, the di-N-acyl derivative of 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic (pseudaminic) acid. Formyl, acetyl and (R)-3-hydroxybutyryl groups were identified as the N-acyl substituents of the last monosaccharide; O5a,b,c and O5a,b,d lipopolysaccharides also contained O-acetyl groups. The glycosidic linkage of pseudaminic acid was extremely labile towards acids, and mild acid degradation of the lipopolysaccharides produced, instead of the O-specific polysaccharides, their trisaccharide fragments with pseudaminic acid at the reducing terminus. Similar degradation of immunotype 6 lipopolysaccharides, followed by oxidation with sodium metaperiodate, resulted in a disaccharide fragment due to destruction of xylose. In contrast the glycosidic linkage of pseudaminic acid proved to be more stable towards treatment with hydrogen fluoride than those of xylose and N-acetylfucosamine. As a result, solvolysis of immunotype 6 lipopolysaccharide with hydrogen fluoride in methanol gave methyl glycosides of a disaccharide and a trisaccharide with pseudaminic acid at the non-reducing terminus. Mild acid hydrolysis of these oligosides afforded free 5-N-acetyl-7-N-formylpseudaminic acid, which was identified by the 1H ande 13C nuclear magnetic resonance data, as well as by the mass spectrum of the corresponding fully methylated aldonic acid. As a result of the identification of all oligosaccharides obtained and comparative analysis of the 13C nuclear magnetic resonance spectra of the oligosaccharides and lipopolysaccharides the following structures were established for the repeating units of the polysaccharide chains of the lipopolysaccharides: (Formula: see text) where D-Xyl = D-xylose, D-FucNAc = 2-acetamido-2,6-dideoxy-D-galactose, Pse5N7NFm = 5-amino-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid (7-N-formylpseudaminic acid). All the polysaccharides have an identical carbohydrate skeleton and differ from each other by the acyl substituent at N-5 of pseudaminic acid [acetyl or (R)-3-hydroxybutyryl group] or by the presence or absence of the O-acetyl group at position 4 of N-acetylfucosamine. The data obtained account properly for the O specificity of the studied P. aeruginosa strains.

  NCBI PubMed ID: 3104041
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Methods: 13C NMR, 1H NMR
  
   
  
  Pseudomonas aeruginosa 5a, Pseudomonas aeruginosa 5b, Pseudomonas aeruginosa 5d, Pseudomonas aeruginosa Lányi
  CSDB ID 123025 (all data & tools)
• Article ID: 3207
  Knirel YA, Bystrova OV, Kocharova NA, Zähringer U, Pier GB "Conserved and variable structural features of the Pseudomonas aeruginosa lipopolysaccharide" - Journal of Endotoxin Research 12(6) (2006) 324-336
  

  The review is devoted to recent progress in the structural elucidation of the lipopolysaccharide of the bacterium Pseudomonas aeruginosa, including O-antigen biological repeats, core oligosaccharide, and lipid A. Data on biosynthesis, genetics and serology of the lipopolysaccharide isolated from various P. aeruginosa O-serogroups are discussed in relation to the chemical structures.

  O-antigen, Pseudomonas aeruginosa, lipid A, core oligosaccharide, lipopolysaccharide structure, serologic activity

  NCBI PubMed ID: 17254386
  Publication DOI: 10.1179/096805106X118906
  Journal NLM ID: 9433350
  Publisher: Maney Publishing
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
  Methods: NMR, chemical methods, MS, serological methods, genetic methods
  
   
  
  Pseudomonas aeruginosa O8 O7a,7b,7d
  CSDB ID 20572 (all data & tools)
• Article ID: 3711
  King JD, Kocincova D, Westman EL, Lam JS "Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa" - Innate Immunity 15(5) (2009) 261-312
  

  Pseudomonas aeruginosa causes serious nosocomial infections, and an important virulence factor produced by this organism is lipopolysaccharide (LPS). This review summarizes knowledge about biosynthesis of all three structural domains of LPS - lipid A, core oligosaccharide, and O polysaccharides. In addition, based on similarities with other bacterial species, this review proposes new hypothetical pathways for unstudied steps in the biosynthesis of P. aeruginosa LPS. Lipid A biosynthesis is discussed in relation to Escherichia coli and Salmonella, and the biosyntheses of core sugar precursors and core oligosaccharide are summarised. Pseudomonas aeruginosa attaches a Common Polysaccharide Antigen and O-Specific Antigen polysaccharides to lipid A-core. Both forms of O polysaccharide are discussed with respect to their independent synthesis mechanisms. Recent advances in understanding O-polysaccharide biosynthesis since the last major review on this subject, published nearly a decade ago, are highlighted. Since P. aeruginosa O polysaccharides contain unusual sugars, sugar-nucleotide biosynthesis pathways are reviewed in detail. Knowledge derived from detailed studies in the O5, O6 and O11 serotypes is applied to predict biosynthesis pathways of sugars in poorly-studied serotypes, especially O1, O4, and O13/O14. Although further work is required, a full understanding of LPS biosynthesis in P. aeruginosa is almost within reach.

  Lipopolysaccharide, core, O-antigen, Pseudomonas aeruginosa, lipid A

  NCBI PubMed ID: 19710102
  Publication DOI: 10.1177/1753425909106436
  Journal NLM ID: 101469670
  Publisher: Sage Publications
  Correspondence: jlam@uoguelph.ca
  Institutions: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
  
   
  
  Pseudomonas aeruginosa O8
  CSDB ID 24036 (all data & tools)
• Article ID: 3873
  Knirel YA, Bystrova OV, Kocharova NA, Zähringer U, Pier GB "Corrigendum: Conserved and variable structural features in the lipopolysaccharide of Pseudomonas aeruginosa" - Innate Immunity 16(4) (2010) 274
  

  The review is devoted to recent progress in the structural elucidation of the lipopolysaccharide of the bacterium Pseudomonas aeruginosa, including O-antigen biological repeats, core oligosaccharide, and lipid A. Data on biosynthesis, genetics and serology of the lipopolysaccharide isolated from various P. aeruginosa O-serogroups are discussed in relation to the chemical structures.

  Lipopolysaccharide, structure, Pseudomonas aeruginosa, core oligosaccharide, variable

  Publication DOI: 10.1177/1753425910369459
  Journal NLM ID: 101469670
  Publisher: Sage Publications
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Pseudomonas aeruginosa O7a,7b,7d, Pseudomonas aeruginosa 8
  CSDB ID 25718 (all data & tools)
• Article ID: 4062
  Lam JS, Taylor VL, Islam ST, Hao Y, Kocincova D "Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide" - Frontiers in Microbiology 2 (2011) 118
  

  Lipopolysccharide (LPS) is an integral component of the Pseudomonas aeruginosa cell envelope, occupying the outer leaflet of the outer membrane in this Gram-negative opportunistic pathogen. It is important for bacterium-host interactions and has been shown to be a major virulence factor for this organism. Structurally, P. aeruginosa LPS is composed of three domains, namely, lipid A, core oligosaccharide, and the distal O antigen (O-Ag). Most P. aeruginosa strains produce two distinct forms of O-Ag, one a homopolymer of D-rhamnose that is a common polysaccharide antigen (CPA, formerly termed A band), and the other a heteropolymer of three to five distinct (and often unique dideoxy) sugars in its repeat units, known as O-specific antigen (OSA, formerly termed B band). Compositional differences in the O units among the OSA from different strains form the basis of the International Antigenic Typing Scheme for classification via serotyping of different strains of P. aeruginosa. The focus of this review is to provide state-of-the-art knowledge on the genetic and resultant functional diversity of LPS produced by P. aeruginosa. The underlying factors contributing to this diversity will be thoroughly discussed and presented in the context of its contributions to host-pathogen interactions and the control/prevention of infection.

  Lipopolysaccharide, biosynthesis, virulence, serotyping, bacteriophage, motility, seroconversion, nucleotide sugars

  NCBI PubMed ID: 21687428
  Publication DOI: 10.3389/fmicb.2011.00118
  Journal NLM ID: 101548977
  Publisher: Lausanne: Frontiers Research Foundation
  Correspondence: jlam@uoguelph.ca
  Institutions: Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
  
   
  
  Pseudomonas aeruginosa O8
  CSDB ID 26869 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_114701,IEDB_167188,IEDB_174332

• Article ID: 1470
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Pseudomonas aeruginosa O7a,7d
  CSDB ID 31922 (all data & tools)
• Article ID: 1838
  Knirel YA, Kocharova NA, Shashkov AS, Dmitriev BA, Kochetkov NK, Stanislavsky ES, Mashilova GM "Antigenic polysaccharides of bacteria. 18. Structure of O-specific polysaccharide chains of Pseudomonas aeruginosa O5 (Lanyi) lipopolysaccharides" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 12 (1986) 1384-1390
  

  Polysaccharide chains of P. aeruginosa O5a, b, c, O5a, b, d and O5a, d (Lányi classification) lipopolysaccharides contain D-xylose, N-acetyl-D-fucosamine (FucNAc) and a derivative of 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic acid (pseudaminic acid, PseN2) carrying acetyl or (R)-3-hydroxybutyryl (Hb) and formyl (Fm) groups as N-acyl substituents. Degradation of the lipopolysaccharides with dilute acetic acid caused depolymerisation of the polysaccharide chains as a result of cleavage of glycosidic linkage of pseudaminic acid to give trisaccharides representing chemical repeating units of the polysaccharides. Basing on analysis of the trisaccharides using 1H and 13C NMR spectroscopy and mass-spectrometry, the following structures of the polysaccharide chains were established: (Formula: see text). O5a, d polysaccharide is identical to P. aeruginosa immunotype 6 O-specific polysaccharide.

  NCBI PubMed ID: 2434100
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
  Methods: 13C NMR
  
   
  
  Pseudomonas aeruginosa O5a,d, Pseudomonas aeruginosa 6
  CSDB ID 110556 (all data & tools)
• Article ID: 2054
  Knirel YA, Kocharova NA, Shashkov AS, Kochetkov NK "The structure of the Pseudomonas aeruginosa immunotype 6 O-antigen: isolation and identification of 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid" - Carbohydrate Research 145 (1986) C1-C4
  
  NCBI PubMed ID: 2420447
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
  Methods: 13C NMR
  
   
  
  Pseudomonas aeruginosa 6
  CSDB ID 114549 (all data & tools)
• Article ID: 2403
  Knirel YA, Kocharova NA, Shashkov AS, Dmitriev BA, Kochetkov NK, Stanislavsky ES, Mashilova GM "Somatic antigens of Pseudomonas aeruginosa. The structure of O-specific polysaccharide chains of the lipopolysaccharides from P.aeruginosa O5 (Lányi) and immunotype 6 (Fisher)" - European Journal of Biochemistry 163 (1987) 639-652
  

  Lipopolysaccharides were isolated from dry bacterial cells of Pseudomonas aeruginosa O5a,b,c, O5a,b,d, O5a,d (Lányi classification) and immunotype 6 (Fisher classification) by the Westphal procedure. Their polysaccharide chains were built up of trisaccharide repeating units containing D-xylose, 2-acetamido-2,6-dideoxy-D-galactose and a new sialic acid-like sugar, the di-N-acyl derivative of 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic (pseudaminic) acid. Formyl, acetyl and (R)-3-hydroxybutyryl groups were identified as the N-acyl substituents of the last monosaccharide; O5a,b,c and O5a,b,d lipopolysaccharides also contained O-acetyl groups. The glycosidic linkage of pseudaminic acid was extremely labile towards acids, and mild acid degradation of the lipopolysaccharides produced, instead of the O-specific polysaccharides, their trisaccharide fragments with pseudaminic acid at the reducing terminus. Similar degradation of immunotype 6 lipopolysaccharides, followed by oxidation with sodium metaperiodate, resulted in a disaccharide fragment due to destruction of xylose. In contrast the glycosidic linkage of pseudaminic acid proved to be more stable towards treatment with hydrogen fluoride than those of xylose and N-acetylfucosamine. As a result, solvolysis of immunotype 6 lipopolysaccharide with hydrogen fluoride in methanol gave methyl glycosides of a disaccharide and a trisaccharide with pseudaminic acid at the non-reducing terminus. Mild acid hydrolysis of these oligosides afforded free 5-N-acetyl-7-N-formylpseudaminic acid, which was identified by the 1H ande 13C nuclear magnetic resonance data, as well as by the mass spectrum of the corresponding fully methylated aldonic acid. As a result of the identification of all oligosaccharides obtained and comparative analysis of the 13C nuclear magnetic resonance spectra of the oligosaccharides and lipopolysaccharides the following structures were established for the repeating units of the polysaccharide chains of the lipopolysaccharides: (Formula: see text) where D-Xyl = D-xylose, D-FucNAc = 2-acetamido-2,6-dideoxy-D-galactose, Pse5N7NFm = 5-amino-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid (7-N-formylpseudaminic acid). All the polysaccharides have an identical carbohydrate skeleton and differ from each other by the acyl substituent at N-5 of pseudaminic acid [acetyl or (R)-3-hydroxybutyryl group] or by the presence or absence of the O-acetyl group at position 4 of N-acetylfucosamine. The data obtained account properly for the O specificity of the studied P. aeruginosa strains.

  NCBI PubMed ID: 3104041
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Methods: 13C NMR, 1H NMR
  
   
  
  Pseudomonas aeruginosa 6, Pseudomonas aeruginosa Fisher
  CSDB ID 123024 (all data & tools)
• Article ID: 3207
  Knirel YA, Bystrova OV, Kocharova NA, Zähringer U, Pier GB "Conserved and variable structural features of the Pseudomonas aeruginosa lipopolysaccharide" - Journal of Endotoxin Research 12(6) (2006) 324-336
  

  The review is devoted to recent progress in the structural elucidation of the lipopolysaccharide of the bacterium Pseudomonas aeruginosa, including O-antigen biological repeats, core oligosaccharide, and lipid A. Data on biosynthesis, genetics and serology of the lipopolysaccharide isolated from various P. aeruginosa O-serogroups are discussed in relation to the chemical structures.

  O-antigen, Pseudomonas aeruginosa, lipid A, core oligosaccharide, lipopolysaccharide structure, serologic activity

  NCBI PubMed ID: 17254386
  Publication DOI: 10.1179/096805106X118906
  Journal NLM ID: 9433350
  Publisher: Maney Publishing
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
  Methods: NMR, chemical methods, MS, serological methods, genetic methods
  
   
  
  Pseudomonas aeruginosa O7a,7d, Pseudomonas aeruginosa F6
  CSDB ID 12730 (all data & tools)
• Article ID: 3873
  Knirel YA, Bystrova OV, Kocharova NA, Zähringer U, Pier GB "Corrigendum: Conserved and variable structural features in the lipopolysaccharide of Pseudomonas aeruginosa" - Innate Immunity 16(4) (2010) 274
  

  The review is devoted to recent progress in the structural elucidation of the lipopolysaccharide of the bacterium Pseudomonas aeruginosa, including O-antigen biological repeats, core oligosaccharide, and lipid A. Data on biosynthesis, genetics and serology of the lipopolysaccharide isolated from various P. aeruginosa O-serogroups are discussed in relation to the chemical structures.

  Lipopolysaccharide, structure, Pseudomonas aeruginosa, core oligosaccharide, variable

  Publication DOI: 10.1177/1753425910369459
  Journal NLM ID: 101469670
  Publisher: Sage Publications
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Pseudomonas aeruginosa O7a,7d, Pseudomonas aeruginosa 6
  CSDB ID 25719 (all data & tools)
• Article ID: 4684
  Islam ST, Lam JS "Synthesis of bacterial polysaccharides via the Wzx/Wzy-dependent pathway" - Canadian Journal of Microbiology 60(11) (2014) 697-716
  

  The surfaces of bacteria mediate a multitude of functions in the environment and in an infected host, including adhesion to both biotic and abiotic substrata, motility, immune system interaction and (or) activation, biofilm formation, and cell-cell communication, with many of these features directly influenced by cell-surface glycans. In both Gram-negative and Gram-positive bacteria, the majority of cell-surface polysaccharides are produced via the Wzx/Wzy-dependent assembly pathway; these glycans include heteropolymeric O-antigen, enterobacterial common antigen, exopolysaccharide, spore coat, and capsule in diverse bacteria. The key components of this assembly pathway are the integral inner membrane Wzx flippase, Wzy polymerase, and Wzz chain-length regulator proteins, which until recently have resisted detailed structural and functional characterization. In this review, we have provided a comprehensive synthesis of the latest structural and mechanistic data for each protein, as well as an examination of substrate specificity for each assembly step and complex formation between the constituent proteins. To complement the unprecedented explosion of genomic-sequencing data for bacteria, we have also highlighted both classical and state-of-the-art methods by which encoded Wzx, Wzy, and Wzz proteins can be reliably identified and annotated, using the model Gram-negative bacterium Pseudomonas aeruginosa as an example data set. Lastly, we outline future avenues of research, with the aim of stimulating researchers to take the next steps in investigating the function of, and interplay between, the constituents of this widespread assembly scheme.

  Membrane Proteins, lipopolysaccharide (LPS), Wzx flippase, Wzy polymerase, Wzz polysaccharide copolymerase

  NCBI PubMed ID: 25358682
  Publication DOI: 10.1139/cjm-2014-0595
  Journal NLM ID: 0372707
  Publisher: National Research Council of Canada
  Correspondence: sislam@imm.cnrs.fr; jlam@uoguelph.ca
  Institutions: Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
  Methods: SDS-PAGE, genetic methods, cloning
  
   
  
  Pseudomonas aeruginosa O8
  CSDB ID 30282 (all data & tools)
• Article ID: 6201
  Banahene N, Kavunja HW, Swarts BM "Chemical reporters for bacterial glycans: development and applications" - Chemical Reviews 122(3) (2022) 3336-3413
  

  Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species-including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.

  biosynthesis, glycoconjugates, glycan, polysaccharides, Gram-negative bacteria, gram-positive bacteria

  NCBI PubMed ID: 34905344
  Publication DOI: 10.1021/acs.chemrev.1c00729
  Journal NLM ID: 2985134R
  Publisher: Chem Rev
  Correspondence: ben.swarts@cmich.edu
  Institutions: Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, United States, Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, Michigan 48859, United States
  
   
  
  Pseudomonas aeruginosa O7a,7d
  CSDB ID 20822 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: pilin
Trivial name: tisaccharide chain of pilin
Compound class: O-glycoprotein
Contained glycoepitopes: IEDB_114701,IEDB_150900,IEDB_167188,IEDB_174332

• Article ID: 1470
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Pseudomonas aeruginosa 1244
  CSDB ID 31923 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136095,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_983931,SB_192,SB_7

• Article ID: 1470
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Shigella boydii 7
  CSDB ID 31924 (all data & tools)
• Article ID: 1845
  L'vov VL, Shashkov AS, Dmitriev BA "Bacterial antigenic polysaccharides. The structure of the repeating unit of the specific polysaccharide from Shigella boydii type 7" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 13 (1987) 223-233
  

  Acid hydrolysis of the antigenic lipopolysaccharide from Shigella boydii type 7 afforded a specific polysaccharide composed of 2-acetamido-2-deoxy-D-glucose, D-glucose, D-galactose, 5-acetamido-3,5,7,9-tetradeoxy-7-[(3R)-3-hydroxybutyramido]-L-glycero-L-manno-nonulosonic acid (NonN2A) and acetic acid residues in the 1:1:2:1:1 ratio. From the results of methylation analysis, hydrogen fluoride solvolysis and Smith degradation, the structure of the repeating unit of the specific polysaccharide was dedused as: -2) Galf (β1-3)GlcNAcp (α1-8)NonN2A(4Ac) (β2-6) Galp (α1-6) Glcp (α1-. The 13C NMR spectrum of the polysaccharide was interpreted, and the spectral data fully confirmed the structure of the polysaccharide repeating unit.

  NCBI PubMed ID: 2437931
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
  Methods: 13C NMR
  
   
  
  Shigella boydii 7
  CSDB ID 110596 (all data & tools)
• Article ID: 5760
  Dobrochaeva K, Khasbiulina N, Shilova N, Antipova N, Obukhova P, Galanina O, Blixt O, Kunz H, Filatov A, Knirel Y, Le Pendu J, Khaidukov S, Bovin N "Specificity of human natural antibodies referred to as anti-Tn" - Molecular Immunology 120 (2020) 74-82
  

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

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

  NCBI PubMed ID: 32087569
  Publication DOI: 10.1016/j.molimm.2020.02.005
  Journal NLM ID: 7905289
  Publisher: Elsevier
  Correspondence: professorbovin@yandex.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, Moscow, Russian Federation, Semiotik LLC, 16/10 Miklukho-Maklaya, Moscow, Russian Federation, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation, National Research University Higher School of Economics, Moscow, Russian Federation, Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark, Institut Fur Organische Chemie, Johannes Gutenberg-Universitat Mainz, Duesbergweg 10-14, D-55128, Mainz, Germany, Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, Russian Federation, University of Nantes, Inserm, U892 IRT UN, 8 Quai MonCousu, BP70721 Nantes, FR 44007, France
  Methods: ELISA, affinity chromatography, flow cytometry analysis, printed glycan array (PGA) analysis, FACS assay
  
   
  
  Shigella boydii 7
  CSDB ID 3984 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137473,IEDB_140630

• Article ID: 1470
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Pseudoalteromonas distincta KMM 638
  CSDB ID 31928 (all data & tools)