Show legend Show as text

Structure type: polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_885822

• Article ID: 32
  Bystrova OV, Lindner B, Moll H, Kocharova NA, Knirel YA, Zähringer U, Pier GB "Structure of the biological repeating unit of the O-antigen of Pseudomonas aeruginosa immunotype 4 containing both 2-acetamido-2,6-dideoxy-D-glucose and 2-acetamido-2,6-dideoxy-D-galactose" - Carbohydrate Research 338(17) (2003) 1801-1806
  

  A phosphorylated core-lipid A backbone oligosaccharide that carries a disaccharide remainder of the first O-antigen repeating unit was derived by strong alkaline degradation following mild hydrazinolysis of the lipopolysaccharide of Pseudomonas aeruginosa immunotype 4 (serogroup O-1). The structure of the oligosaccharide was determined using ESI MS and NMR spectroscopy and it was demonstrated that 2-acetamido-2,6-dideoxy-D-glucose is the first monosaccharide of the O-polysaccharide that is linked to the LPS core. These data define the structure of the biological repeating unit of the O-antigen

  Lipopolysaccharide, structure, O-antigen, repeating unit, Pseudomonas aeruginosa, O-polysaccharide, 2-acetamido-2, 6-dideoxy-D-galactose

  NCBI PubMed ID: 12892948
  Publication DOI: 10.1016/S0008-6215(03)00262-3
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
  Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR, ESI-MS, GLC, alkaline degradation
  
   
  
  Pseudomonas aeruginosa 4
  CSDB ID 1820 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: O-polysaccharide, O-antigen

• Article ID: 37
  Caroff M, Karibian D "Structure of bacterial lipopolysaccharides" - Carbohydrate Research 338(23) (2003) 2431-2447
  

  Bacterial lipopolysaccharides are the major components of the outer surface of Gram-negative bacteria They are often of interest in medicine for their immunomodulatory properties. In small amounts they can be beneficial, but in larger amounts they may cause endotoxic shock. Although they share a common architecture, their structural details exert a strong influence on their activity. These molecules comprise: a lipid moiety, called lipid A, which is considered to be the endotoxic component, a glycosidic part consisting of a core of approximately 10 monosaccharides and, in 'smooth-type' lipopolysaccharides, a third region, named O-chain, consisting of repetitive subunits of one to eight monosaccharides responsible for much of the immunospecificity of the bacterial cell.

  Lipopolysaccharide, structure, core, lipid A, endotoxin, O-chains

  NCBI PubMed ID: 14670707
  Publication DOI: 10.1016/j.carres.2003.07.010
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: martine.carloff@bbmpc.u-psud.fr
  Institutions: Equipe Endotoxines, UMR 8619 du Centre National de la Recherche Scientifique, IBBMC, Université de Paris-Sud, F-Orsay, France
  
   
  
  Bordetella avium ATCC 5086
  CSDB ID 31484 (all data & tools)
• Article ID: 3697
  Harvey DJ "Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2003-2004" - Mass Spectrometry Reviews 28(2) (2009) 273-361
  

  This review is the third update of the original review, published in 1999, on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings the topic to the end of 2004. Both fundamental studies and applications are covered. The main topics include methodological developments, matrices, fragmentation of carbohydrates and applications to large polymeric carbohydrates from plants, glycans from glycoproteins and those from various glycolipids. Other topics include the use of MALDI MS to study enzymes related to carbohydrate biosynthesis and degradation, its use in industrial processes, particularly biopharmaceuticals and its use to monitor products of chemical synthesis where glycodendrimers and carbohydrate-protein complexes are highlighted

  carbohydrates, glycosyltransferases, fragmentation, MALDI, glycolipids, glycoproteins, biopharmaceuticals, glycosidases, time-of-flight

  NCBI PubMed ID: 18825656
  Publication DOI: 10.1002/mas.2019
  Journal NLM ID: 8219702
  Publisher: Wiley
  Correspondence: david.harvey@bioch.ox.ac.uk
  Institutions: Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK
  Methods: NMR, MALDI-TOF MS
  
   
  
  Bordetella avium ATCC 5086
  CSDB ID 24006 (all data & tools)
• Article ID: 5742
  Caroff M, Novikov A "Lipopolysaccharides: structure, function and bacterial identification" - OCL - Oilseeds and fats, Crops and Lipids 27 (2020) 31
  

  Lipopolysaccharides (LPS) are the main components of the outer membrane of Gram-negative bacteria. They are glycolipids containing a lipid moiety called lipid A, more often made of a bis-phosphorylated glucosamine disaccharide, carrying fatty acids in ester and amide linkages. Lipid A is linked to a core oligosaccharide of about 10 sugars, substituted in the wild-type strains, by long-chain oligosaccharide repetitive units, extending outside the bacteria and representing their main antigens. In addition to determine the serotype of the bacterium, LPS are highly potent biological molecules, capable of eliciting at the level of minute amounts, beneficial, as well as deleterious activities.

  Lipopolysaccharide, serology, endotoxins, inflammation, structure-activity

  Publication DOI: 10.1051/ocl/2020025
  Publisher: France: EDP Sciences (ISSN: 22726977, 22576614)
  Correspondence: martine.caroff@lpsbiosciences.com
  Institutions: LPS-BioSciences, Paris-Saclay University, Orsay, France, Hephaistos-Pharma, Paris-Saclay University, Orsay, France
  
   
  
  Bordetella avium ATCC5086
  CSDB ID 3311 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide

• Article ID: 182
  Vinogradov E "Structure of the O-specific polysaccharide chain of the lipopolysaccharide of Bordetella hinzii" - Carbohydrate Research 337(10) (2002) 961-963
  

  The lipopolysaccharide of Bordetella hinzii was analyzed after various chemical degradations by NMR spectroscopy and MALDI mass spectrometry, and the following structure of the polysaccharide chain was determined: 4-O-Me-α-GalpNAc3NAcAN-(1→[→4)-β-GlcpNAc3NAcAN-(1→4)-β-GlcpNAc3NAcAN-(1→4)-α-GalpNAc3NAcAN-(1-](n)-where GlcNAc3NAcAN and GalNAc3NAcAN stand for 2,3-diacetamido-2,3-dideoxy-glucuronamide and -galacturonamide, respectively. The polysaccharide chain is terminated with a 4-O-methylated GalNAc3NAcAN residue and is rather short (n < or = 5).

  Lipopolysaccharide, O-specific polysaccharide, polysaccharide structure, Bordetella hinzii

  NCBI PubMed ID: 12007480
  Publication DOI: 10.1016/s0008-6215(02)00071-x
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: evguenii.vinogradov@nrc.ca
  Institutions: Institute for Biological Sciences, National Research Council, 100 Sussex Drive, Ottawa, Ont., Canada K 1A 0R 6
  Methods: NMR-2D, NMR, MALDI-MS, chemical methods
  
   
  
  Bordetella hinzii ATCC 51730
  CSDB ID 5512 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Trivial name: polysaccharide part of a glycoconjugate, glycan repeating unit of the glycoconjugate
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 806
  Hashimoto M, Asai Y, Jinno T, Adachi S, Kusumoto S "Structural elucidation of polysaccharide part of glycoconjugate from Treponema medium ATCC700293" - European Journal of Biochemistry 270 (2003) 2671-2679
  

  Glycoconjugates are distributed on the cell surfaces of some small-sized treponemes and have been reported to be completely different from lipopolysaccharides. We separated a glycoconjugate fraction from Treponema medium ATCC700293, a medium-sized oral spirochete, to assess its immunobiological activities and elucidate the chemical structure of its polysaccharide part using phenol/water extraction, hydrophobic chromatography, and gel .ltration. The glycoconjugate showed negligible or weak endotoxic and immunobiological properties. The chemical structure of the polysaccharide part was shown by two-dimensional NMR and MALDI-TOF-MS to be a tetrasaccharide backbone with two amino acids: -4)[Ac(1-3),Ac(1-2)]bDGlcpN3NA(1-4)[xLOrn(6-6)Ac(1-2)]bDManpN3NA(1-3)[Ac(1-2)]bDGlcpN(1-3)[xDAsp?(1-4)]aDFucp4N(1-.

  structural, polysaccharide, aspartic acid, MALDI-TOF MS, ornithine, glycoconjugate, medium, Treponema

  NCBI PubMed ID: 12787034
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: tomo527@dent.asahi-u.ac.jp
  Institutions: Department of Oral Microbiology, Asahi University School of Dentistry, Gifu, Japan, Graduate School of Science, Osaka University, Osaka, Japan
  Methods: NMR-2D, ESI-MS, MALDI-TOF MS
  
   
  
  Treponema medium ATCC 700293
  CSDB ID 2403 (all data & tools)
• Article ID: 3697
  Harvey DJ "Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2003-2004" - Mass Spectrometry Reviews 28(2) (2009) 273-361
  

  This review is the third update of the original review, published in 1999, on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings the topic to the end of 2004. Both fundamental studies and applications are covered. The main topics include methodological developments, matrices, fragmentation of carbohydrates and applications to large polymeric carbohydrates from plants, glycans from glycoproteins and those from various glycolipids. Other topics include the use of MALDI MS to study enzymes related to carbohydrate biosynthesis and degradation, its use in industrial processes, particularly biopharmaceuticals and its use to monitor products of chemical synthesis where glycodendrimers and carbohydrate-protein complexes are highlighted

  carbohydrates, glycosyltransferases, fragmentation, MALDI, glycolipids, glycoproteins, biopharmaceuticals, glycosidases, time-of-flight

  NCBI PubMed ID: 18825656
  Publication DOI: 10.1002/mas.2019
  Journal NLM ID: 8219702
  Publisher: Wiley
  Correspondence: david.harvey@bioch.ox.ac.uk
  Institutions: Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK
  Methods: NMR, MALDI-TOF MS
  
   
  
  Treponema medium
  CSDB ID 23709 (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
  
   
  
  Treponema medium ATCC 700293
  CSDB ID 21178 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: repeating unit of the glycoconjugate polysaccharide part
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 806
  Hashimoto M, Asai Y, Jinno T, Adachi S, Kusumoto S "Structural elucidation of polysaccharide part of glycoconjugate from Treponema medium ATCC700293" - European Journal of Biochemistry 270 (2003) 2671-2679
  

  Glycoconjugates are distributed on the cell surfaces of some small-sized treponemes and have been reported to be completely different from lipopolysaccharides. We separated a glycoconjugate fraction from Treponema medium ATCC700293, a medium-sized oral spirochete, to assess its immunobiological activities and elucidate the chemical structure of its polysaccharide part using phenol/water extraction, hydrophobic chromatography, and gel .ltration. The glycoconjugate showed negligible or weak endotoxic and immunobiological properties. The chemical structure of the polysaccharide part was shown by two-dimensional NMR and MALDI-TOF-MS to be a tetrasaccharide backbone with two amino acids: -4)[Ac(1-3),Ac(1-2)]bDGlcpN3NA(1-4)[xLOrn(6-6)Ac(1-2)]bDManpN3NA(1-3)[Ac(1-2)]bDGlcpN(1-3)[xDAsp?(1-4)]aDFucp4N(1-.

  structural, polysaccharide, aspartic acid, MALDI-TOF MS, ornithine, glycoconjugate, medium, Treponema

  NCBI PubMed ID: 12787034
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: tomo527@dent.asahi-u.ac.jp
  Institutions: Department of Oral Microbiology, Asahi University School of Dentistry, Gifu, Japan, Graduate School of Science, Osaka University, Osaka, Japan
  Methods: NMR-2D, ESI-MS, MALDI-TOF MS
  
   
  
  Treponema medium ATCC 700293
  CSDB ID 2553 (all data & tools)

Show legend Show as text

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

• Article ID: 872
  Kocharova NA, Perepelov AV, Zatonsky GV, Shashkov AS, Knirel YA, Jansson P, Weintraub A "Structural studies of the O-specific polysaccharide of Vibrio cholerae O8 using solvolysis with triflic acid" - Carbohydrate Research 330(1) (2001) 83-92
  

  The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: →4)-β-D-Glcp NAc3NAcylAN-(1→4)-β-D-Manp NAc3NAcAN-(1→4)-α-L-Gulp NAc3NAcA-(1→3)-β-D-QuipNAc4NAc-(1→ where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of β-QuiNAc4NAc and α-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.

  Lipopolysaccharide, O-specific polysaccharide, O-Specific polysaccharide structure, 2, 3-diamino-2, Vibrio cholerae, 3-dideoxyhexuronic acid, triflic acid solvolysis, solvolysis

  NCBI PubMed ID: 11217966
  Publication DOI: 10.1016/S0008-6215(00)00271-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pererik.jansson@kfcmail.hs.sii.se
  Institutions: Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  Methods: NMR, HF solvolysis, ESI-MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 2836 (all data & tools)
• Article ID: 1452
  Chatterjee SN, Chaudhuri K "Lipopolysaccharides of Vibrio cholerae. I. Physical and chemical characterization" - Biochimica et Biophysica Acta 1639(2) (2003) 65-79
  

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

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

  NCBI PubMed ID: 14559113
  Publication DOI: 10.1016/j.bbadis.2003.08.004
  Journal NLM ID: 0217513
  Publisher: Elsevier
  Correspondence: sncac@sify.com (S.N. Chatterjee)
  Institutions: Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Sector-1, Calcutta-700 064, India, Biophysics Division, Indian Institute of Chemical Biology, Jadavpur, Calcutta-700 032, India
  
   
  
  Vibrio cholerae O8
  CSDB ID 31698 (all data & tools)
• Article ID: 1469
  Knirel YA, Perepelov AV "Trifluoromethanesulfonic acid: a useful reagent for the solvolytic cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Australian Journal of Chemistry 55(1-2) (2002) 69-72
  

  The initial data on the application of triflic acid was summarized for the isolation of complex monosachharide derivatives and oligosachharides in the structural analysis of various bacterial polysachharides. Solvolysis proceeded selectively and without destruction of the sugars. Varying the temperature and duration of the reaction enabled preparation of oligosaccharides of different sizes.

  polysaccharide, structural analysis, bacterial polysaccharides, solvolysis, trifluoromethanesulfonic acid, triflic acid

  Publication DOI: 10.1071/CH01181
  Journal NLM ID: 0370614
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: 13C NMR, 1H NMR, GLC, MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 31914 (all data & tools)
• Article ID: 4329
  Knirel YA "Structure of O-antigens" - Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
  

  The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.

  Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis

  Publication DOI: 10.1007/978-3-7091-0733-1_3
  Publisher: Springer
  Correspondence: knirel@ioc.ac.ru
  Editors: Knirel YA, Valvano MA
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Vibrio cholerae O8
  CSDB ID 27772 (all data & tools)
• Article ID: 5157
  Goyette-Desjardins G, Vinogradov E, Okura M, Takamatsu D, Gottschalk M, Segura M "Streptococcus suis serotype 3 and serotype 18 capsular polysaccharides contain di-N-acetyl-bacillosamine" - Carbohydrate Research 466 (2018) 18-29
  

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

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

  NCBI PubMed ID: 30014879
  Publication DOI: 10.1016/j.carres.2018.07.003
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: mariela.segura@umontreal.ca
  Institutions: Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., St-Hyacinthe, Quebec, J2S 2M2, Canada, Canadian Glycomics Network (GlycoNet), University of Alberta, 11227 Saskatchewan Dr., Edmonton, Alberta, T6G 2G2, Canada, National Research Council, 100 Sussex Dr., Ottawa, Ontario, K1A 0R6, Canada, Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan, The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu, 501-1193, Japan
  Methods: 13C NMR, 1H NMR, periodate oxidation, gel filtration, NMR-2D, GC-MS, de-O-acylation, sugar analysis, methanolysis, SEC-MALS, bioinformatic analysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 12603 (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
  
   
  
  Vibrio cholerae O8
  CSDB ID 9119 (all data & tools)

Show legend Show as text

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

• Article ID: 872
  Kocharova NA, Perepelov AV, Zatonsky GV, Shashkov AS, Knirel YA, Jansson P, Weintraub A "Structural studies of the O-specific polysaccharide of Vibrio cholerae O8 using solvolysis with triflic acid" - Carbohydrate Research 330(1) (2001) 83-92
  

  The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: →4)-β-D-Glcp NAc3NAcylAN-(1→4)-β-D-Manp NAc3NAcAN-(1→4)-α-L-Gulp NAc3NAcA-(1→3)-β-D-QuipNAc4NAc-(1→ where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of β-QuiNAc4NAc and α-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.

  Lipopolysaccharide, O-specific polysaccharide, O-Specific polysaccharide structure, 2, 3-diamino-2, Vibrio cholerae, 3-dideoxyhexuronic acid, triflic acid solvolysis, solvolysis

  NCBI PubMed ID: 11217966
  Publication DOI: 10.1016/S0008-6215(00)00271-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pererik.jansson@kfcmail.hs.sii.se
  Institutions: Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  Methods: NMR, HF solvolysis, ESI-MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 3033 (all data & tools)

Show legend Show as text

Structure type: oligomer

• Article ID: 872
  Kocharova NA, Perepelov AV, Zatonsky GV, Shashkov AS, Knirel YA, Jansson P, Weintraub A "Structural studies of the O-specific polysaccharide of Vibrio cholerae O8 using solvolysis with triflic acid" - Carbohydrate Research 330(1) (2001) 83-92
  

  The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: →4)-β-D-Glcp NAc3NAcylAN-(1→4)-β-D-Manp NAc3NAcAN-(1→4)-α-L-Gulp NAc3NAcA-(1→3)-β-D-QuipNAc4NAc-(1→ where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of β-QuiNAc4NAc and α-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.

  Lipopolysaccharide, O-specific polysaccharide, O-Specific polysaccharide structure, 2, 3-diamino-2, Vibrio cholerae, 3-dideoxyhexuronic acid, triflic acid solvolysis, solvolysis

  NCBI PubMed ID: 11217966
  Publication DOI: 10.1016/S0008-6215(00)00271-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pererik.jansson@kfcmail.hs.sii.se
  Institutions: Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  Methods: NMR, HF solvolysis, ESI-MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 3034 (all data & tools)

Show legend Show as text

Structure type: oligomer

• Article ID: 872
  Kocharova NA, Perepelov AV, Zatonsky GV, Shashkov AS, Knirel YA, Jansson P, Weintraub A "Structural studies of the O-specific polysaccharide of Vibrio cholerae O8 using solvolysis with triflic acid" - Carbohydrate Research 330(1) (2001) 83-92
  

  The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: →4)-β-D-Glcp NAc3NAcylAN-(1→4)-β-D-Manp NAc3NAcAN-(1→4)-α-L-Gulp NAc3NAcA-(1→3)-β-D-QuipNAc4NAc-(1→ where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of β-QuiNAc4NAc and α-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.

  Lipopolysaccharide, O-specific polysaccharide, O-Specific polysaccharide structure, 2, 3-diamino-2, Vibrio cholerae, 3-dideoxyhexuronic acid, triflic acid solvolysis, solvolysis

  NCBI PubMed ID: 11217966
  Publication DOI: 10.1016/S0008-6215(00)00271-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pererik.jansson@kfcmail.hs.sii.se
  Institutions: Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  Methods: NMR, HF solvolysis, ESI-MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 3035 (all data & tools)

Show legend Show as text

Structure type: oligomer

• Article ID: 872
  Kocharova NA, Perepelov AV, Zatonsky GV, Shashkov AS, Knirel YA, Jansson P, Weintraub A "Structural studies of the O-specific polysaccharide of Vibrio cholerae O8 using solvolysis with triflic acid" - Carbohydrate Research 330(1) (2001) 83-92
  

  The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: →4)-β-D-Glcp NAc3NAcylAN-(1→4)-β-D-Manp NAc3NAcAN-(1→4)-α-L-Gulp NAc3NAcA-(1→3)-β-D-QuipNAc4NAc-(1→ where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of β-QuiNAc4NAc and α-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.

  Lipopolysaccharide, O-specific polysaccharide, O-Specific polysaccharide structure, 2, 3-diamino-2, Vibrio cholerae, 3-dideoxyhexuronic acid, triflic acid solvolysis, solvolysis

  NCBI PubMed ID: 11217966
  Publication DOI: 10.1016/S0008-6215(00)00271-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pererik.jansson@kfcmail.hs.sii.se
  Institutions: Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  Methods: NMR, HF solvolysis, ESI-MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 3036 (all data & tools)

Show legend Show as text

Structure type: oligomer

• Article ID: 872
  Kocharova NA, Perepelov AV, Zatonsky GV, Shashkov AS, Knirel YA, Jansson P, Weintraub A "Structural studies of the O-specific polysaccharide of Vibrio cholerae O8 using solvolysis with triflic acid" - Carbohydrate Research 330(1) (2001) 83-92
  

  The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: →4)-β-D-Glcp NAc3NAcylAN-(1→4)-β-D-Manp NAc3NAcAN-(1→4)-α-L-Gulp NAc3NAcA-(1→3)-β-D-QuipNAc4NAc-(1→ where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of β-QuiNAc4NAc and α-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.

  Lipopolysaccharide, O-specific polysaccharide, O-Specific polysaccharide structure, 2, 3-diamino-2, Vibrio cholerae, 3-dideoxyhexuronic acid, triflic acid solvolysis, solvolysis

  NCBI PubMed ID: 11217966
  Publication DOI: 10.1016/S0008-6215(00)00271-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pererik.jansson@kfcmail.hs.sii.se
  Institutions: Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  Methods: NMR, HF solvolysis, ESI-MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 3037 (all data & tools)

Show legend Show as text

Structure type: oligomer

• Article ID: 872
  Kocharova NA, Perepelov AV, Zatonsky GV, Shashkov AS, Knirel YA, Jansson P, Weintraub A "Structural studies of the O-specific polysaccharide of Vibrio cholerae O8 using solvolysis with triflic acid" - Carbohydrate Research 330(1) (2001) 83-92
  

  The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: →4)-β-D-Glcp NAc3NAcylAN-(1→4)-β-D-Manp NAc3NAcAN-(1→4)-α-L-Gulp NAc3NAcA-(1→3)-β-D-QuipNAc4NAc-(1→ where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of β-QuiNAc4NAc and α-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.

  Lipopolysaccharide, O-specific polysaccharide, O-Specific polysaccharide structure, 2, 3-diamino-2, Vibrio cholerae, 3-dideoxyhexuronic acid, triflic acid solvolysis, solvolysis

  NCBI PubMed ID: 11217966
  Publication DOI: 10.1016/S0008-6215(00)00271-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pererik.jansson@kfcmail.hs.sii.se
  Institutions: Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  Methods: NMR, HF solvolysis, ESI-MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 3038 (all data & tools)

Show legend Show as text

Structure type: oligomer

• Article ID: 872
  Kocharova NA, Perepelov AV, Zatonsky GV, Shashkov AS, Knirel YA, Jansson P, Weintraub A "Structural studies of the O-specific polysaccharide of Vibrio cholerae O8 using solvolysis with triflic acid" - Carbohydrate Research 330(1) (2001) 83-92
  

  The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: →4)-β-D-Glcp NAc3NAcylAN-(1→4)-β-D-Manp NAc3NAcAN-(1→4)-α-L-Gulp NAc3NAcA-(1→3)-β-D-QuipNAc4NAc-(1→ where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of β-QuiNAc4NAc and α-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.

  Lipopolysaccharide, O-specific polysaccharide, O-Specific polysaccharide structure, 2, 3-diamino-2, Vibrio cholerae, 3-dideoxyhexuronic acid, triflic acid solvolysis, solvolysis

  NCBI PubMed ID: 11217966
  Publication DOI: 10.1016/S0008-6215(00)00271-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: pererik.jansson@kfcmail.hs.sii.se
  Institutions: Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  Methods: NMR, HF solvolysis, ESI-MS, triflic acid solvolysis
  
   
  
  Vibrio cholerae O8
  CSDB ID 3039 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_423153

• Article ID: 886
  Komandrova NA, Tomshich SV, Shevchenko LS, Perepelov AV, Senchenkova SN, Shashkov AS, Knirel YA "Structure of an acidic O-specific polysaccharide of the marine bacterium Pseudoalteromonas sp. KMM 634" - Biochemistry (Moscow) 65(9) (2000) 1060-1067
  

  An acidic O-specific polysaccharide containing D-glucuronic acid (D-GlcA), 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid (D-GlcNAc3NAcA), 2,3-diacetamido-2,3-dideoxy-D-mannuronoyl-L-alanine (D-ManNAc3NAcA6Ala), and 2-acetamido-2,4, 6-trideoxy-4-[(S)-3-hydroxybutyramido]-D-glucose (D-QuiNAc4NAcyl) was obtained by mild acid degradation of the lipopolysaccharide of the bacterium Pseudoalteromonas sp. KMM 634 followed by gel-permeation chromatography. The polysaccharide was cleaved selectively with a new solvolytic agent, trifluoromethanesulfonic acid, to give a disaccharide and a trisaccharide with D-GlcNAc3NAcA at the reducing end. The borohydride-reduced oligosaccharides and the initial polysaccharide were studied by GLC-MS and 1H- and 13C NMR spectroscopy, and the following structure of the linear tetrasaccharide repeating unit of the polysaccharide was established: →3)-alpha-D-QuipNAc4Ac4NAcyl-(1→4)-beta-D-ManpNAc3NAcA6Ala-(1→4)-beta-D-GlcpNAc3NAc3NAcA-(1→4)-beta-D-GlcpA-(1→.

  O-antigen, 2-acetamido-2, Bacterial polysaccharide, 2, 4, Pseudoalteromonas haloplanktis, 3-diacetamido-2, 3-dideoxy-D-glucuronic acid, 3-dideoxy-D-mannuronoyl-L-alanine, 6-trideoxy-4-[(S)-3-hydroxybutyramido]-D-glucose, trifluoromethanesulfonic acid

  NCBI PubMed ID: 11042499
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: knirel@ioc.ac.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: GLC-MS, NMR, mild acid hydrolysis, triflic acid solvolysis, borohydride reduction
  
   
  
  Pseudoalteromonas sp. KMM 634
  CSDB ID 2852 (all data & tools)
• Article ID: 1469
  Knirel YA, Perepelov AV "Trifluoromethanesulfonic acid: a useful reagent for the solvolytic cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Australian Journal of Chemistry 55(1-2) (2002) 69-72
  

  The initial data on the application of triflic acid was summarized for the isolation of complex monosachharide derivatives and oligosachharides in the structural analysis of various bacterial polysachharides. Solvolysis proceeded selectively and without destruction of the sugars. Varying the temperature and duration of the reaction enabled preparation of oligosaccharides of different sizes.

  polysaccharide, structural analysis, bacterial polysaccharides, solvolysis, trifluoromethanesulfonic acid, triflic acid

  Publication DOI: 10.1071/CH01181
  Journal NLM ID: 0370614
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: 13C NMR, 1H NMR, GLC, MS, triflic acid solvolysis
  
   
  
  Pseudoalteromonas sp. KMM 634
  CSDB ID 2826 (all data & tools)
• Article ID: 4329
  Knirel YA "Structure of O-antigens" - Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
  

  The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.

  Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis

  Publication DOI: 10.1007/978-3-7091-0733-1_3
  Publisher: Springer
  Correspondence: knirel@ioc.ac.ru
  Editors: Knirel YA, Valvano MA
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Pseudoalteromonas sp. KMM 634
  CSDB ID 27682 (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 sp. KMM 634
  CSDB ID 28821 (all data & tools)
• Article ID: 5461
  Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
  

  This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.

  structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond

  Publication DOI: 10.1070/RCR4856
  Journal NLM ID: 0404506
  Publisher: London: Chemical Society
  Correspondence: Yu.A. Knirel
  Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
  Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudoalteromonas sp. KMM 634
  CSDB ID 1455 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide

• Article ID: 886
  Komandrova NA, Tomshich SV, Shevchenko LS, Perepelov AV, Senchenkova SN, Shashkov AS, Knirel YA "Structure of an acidic O-specific polysaccharide of the marine bacterium Pseudoalteromonas sp. KMM 634" - Biochemistry (Moscow) 65(9) (2000) 1060-1067
  

  An acidic O-specific polysaccharide containing D-glucuronic acid (D-GlcA), 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid (D-GlcNAc3NAcA), 2,3-diacetamido-2,3-dideoxy-D-mannuronoyl-L-alanine (D-ManNAc3NAcA6Ala), and 2-acetamido-2,4, 6-trideoxy-4-[(S)-3-hydroxybutyramido]-D-glucose (D-QuiNAc4NAcyl) was obtained by mild acid degradation of the lipopolysaccharide of the bacterium Pseudoalteromonas sp. KMM 634 followed by gel-permeation chromatography. The polysaccharide was cleaved selectively with a new solvolytic agent, trifluoromethanesulfonic acid, to give a disaccharide and a trisaccharide with D-GlcNAc3NAcA at the reducing end. The borohydride-reduced oligosaccharides and the initial polysaccharide were studied by GLC-MS and 1H- and 13C NMR spectroscopy, and the following structure of the linear tetrasaccharide repeating unit of the polysaccharide was established: →3)-alpha-D-QuipNAc4Ac4NAcyl-(1→4)-beta-D-ManpNAc3NAcA6Ala-(1→4)-beta-D-GlcpNAc3NAc3NAcA-(1→4)-beta-D-GlcpA-(1→.

  O-antigen, 2-acetamido-2, Bacterial polysaccharide, 2, 4, Pseudoalteromonas haloplanktis, 3-diacetamido-2, 3-dideoxy-D-glucuronic acid, 3-dideoxy-D-mannuronoyl-L-alanine, 6-trideoxy-4-[(S)-3-hydroxybutyramido]-D-glucose, trifluoromethanesulfonic acid

  NCBI PubMed ID: 11042499
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: knirel@ioc.ac.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: GLC-MS, NMR, mild acid hydrolysis, triflic acid solvolysis, borohydride reduction
  
   
  
  Pseudoalteromonas sp. KMM 634
  CSDB ID 2947 (all data & tools)
• Article ID: 5461
  Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
  

  This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.

  structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond

  Publication DOI: 10.1070/RCR4856
  Journal NLM ID: 0404506
  Publisher: London: Chemical Society
  Correspondence: Yu.A. Knirel
  Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
  Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudoalteromonas sp. KMM 634
  CSDB ID 1456 (all data & tools)