Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_1391962,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_143794,IEDB_150899,IEDB_151531,IEDB_153216,IEDB_153510,IEDB_190606,IEDB_423153,SB_137,SB_165,SB_166,SB_187,SB_195,SB_29,SB_7,SB_88

• Article ID: 194
  Vinogradov EV, Pantophlet R, Haseley SR, Brade L, Holst O, Brade H "Structural and serological characterisation of the O-specific polysaccharide from lipopolysaccharide of Acinetobacter calcoaceticus strain 7 (DNA group 1)" - European Journal of Biochemistry 243(1-2) (1997) 167-173
  

  S-form lipopolysaccharide was isolated by phenol/water extraction from a strain of Acinetobacter calcoaceticus (DNA group 1). The structure of the O-antigenic polysaccharide was determined by compositional analysis and NMR spectroscopy of the de-O-acylated lipopolysaccharide. The isolated polysaccharide obtained after hydrolysis of lipopolysaccharide in 0.01 M trifluoroacetic acid has the followint structure: [see formula in text] in which Pyr is pyruvate. the O-acetyl substitution of D-Gal was non-stoichiometric. The O-antigen was specifically recognised in wesern blots by polyclonal rabbit antisera.

  Lipopolysaccharide, NMR, DNA, Acinetobacter, Acinetobacter calcoaceticus, O-antigen structure, pyruvate

  NCBI PubMed ID: 9030736
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Division of Biochemical Microbiology, Center for Medicine and Biosciences, Research Center Borstel, Germany
  Methods: NMR-2D, partial acid hydrolysis, NMR, composition analysis, GPC
  
   
  
  Acinetobacter calcoaceticus 7 (DNA group 1)
  CSDB ID 5525 (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
  
   
  
  Acinetobacter calcoaceticus 7
  CSDB ID 9127 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_144989,IEDB_151528,IEDB_153207,IEDB_153216,IEDB_190606,IEDB_885822,SB_165,SB_166,SB_187,SB_195,SB_36,SB_7,SB_88

• Article ID: 915
  Landersjo C, Weintraub A, Ansaruzzaman M, Albert MJ, Widmalm G "Structural analysis of the O-antigenic polysaccharide from Vibrio mimicus N-1990" - European Journal of Biochemistry 251(3) (1998) 986-990
  

  The O-antigenic polysaccharide part of the lipopolysaccharide from Vibrio mimicus N-1990 has been investigated. Sugar and methylation analysis of native and dephosphorylated polysaccharide together with NMR spectroscopy show that the polysaccharide is composed of tetrasaccharide repeating units. The structure of the repeating unit of the polysaccharide from V. mimicus N-1990 could be determined as: →4)-α-D-GalpNAc-(1→3)-β-D-GalpNAc-(1→2)-4,6-P-β-D-Galp-(1→3)-α-D-GalpNAc-(1→. The V. mimicus N-1990 strain cross-reacts with antibodies elicited against the Vibrio cholerae O139. The nature of this cross-reactivity resides in the partial structure comprising the galactosyl residue substituted with a cyclic phosphate. This element is present in the cell-wall-associated polysaccharides of both strains.

  NMR, structure, structural, polysaccharide, analysis, structural analysis, O-antigenic, O-antigenic polysaccharide, Vibrio, cyclic phosphate, Vibrio mimicus

  NCBI PubMed ID: 9490076
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: gw@sg3.organ.su.se
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Sweden, Department of Immunology, Microbiology, Pathology and Infectious Diseases, Division of Clinical and Oral Bacteriology, Karolinska Institute, Huddinge University Hospital, Sweden, International Center for Diarrhoeal Disease Research, Dhaka, Bangladesh
  Methods: NMR-2D, methylation, NMR, sugar analysis, dephosphorylation
  
   
  
  Vibrio mimicus N-1990
  CSDB ID 3111 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: K-antigen
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_150899,IEDB_151531,IEDB_153216,IEDB_153510,IEDB_190606,IEDB_423153,SB_137,SB_165,SB_166,SB_187,SB_195,SB_29,SB_7,SB_88

• Article ID: 2147
  Parolis LA, Parolis H, Dutton GG "Structure of the capsular antigen of Escherichia coli O8:K8:H4" - Carbohydrate Research 193 (1989) 157-163
  

  The structure of the capsular polysaccharide from Escherichia coli O8:K8:H4 has been elucidated, using mainly methylation analysis, Smith degradation, and 1D- and 2D-n.m.r. spectroscopy. The polysaccharide, after removal of bound lipid, was found to be composed of repeating units of the linear tetrasaccharide. (sequence; see text)

  NCBI PubMed ID: 2692813
  Publication DOI: 10.1016/0008-6215(89)85115-8
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: School of Pharmaceutical Sciences, Rhodes University, Grahamstown, South Africa
  Methods: NMR-2D, methylation, Smith degradation
  
   
  
  Escherichia coli K8
  CSDB ID 115765 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_136044,IEDB_136095,IEDB_136794,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_146100,IEDB_149174,IEDB_153216,IEDB_158551,IEDB_190606,SB_126,SB_165,SB_166,SB_170,SB_171,SB_172,SB_187,SB_195,SB_21,SB_25,SB_7,SB_84,SB_88

• Article ID: 3768
  Richards MR, Lowary TL "Chemistry and biology of galactofuranose-containing polysaccharides" - Chembiochem: a European Journal of Chemical Biology 10(12) (2009) 1920-1938
  

  The thermodynamically less stable form of galactose-galactofuranose (Galf)-is essential for the viability of several pathogenic species of bacteria and protozoa but absent in this form in mammals, so the biochemical pathways by which Galf-containing glycans are assembled and catabolysed are attractive sites for drug action. This potential has led to increasing interest in the synthesis of molecules containing Galf residues, their subsequent use in studies directed towards understanding the enzymes that process these residues and the identification of potential inhibitors of these pathways. Major achievements of the past several years have included an in-depth understanding of the mechanism of UDP-galactopyranose mutase (UGM), the enzyme that produces UDP-Galf, which is the donor species for galactofuranosyltransferases. A number of methods for the synthesis of galactofuranosides have also been developed, and practitioners in the field now have many options for the initiation of a synthesis of glycoconjugates containing either α- or β-Galf residues. UDP-Galf has also been prepared by a number of approaches, and it appears that a chemoenzymatic approach is currently the most viable method for producing multi-milligram amounts of this important intermediate. Recent advances both in the understanding of the mechanism of UGM and in the synthesis of galactofuranose and its derivatives are highlighted in this review.

  biosynthesis, carbohydrates, glycoconjugates, glycosylation, organic synthesis

  NCBI PubMed ID: 19591187
  Publication DOI: 10.1002/cbic.200900208
  Journal NLM ID: 100937360
  Publisher: Weinheim, Germany: Wiley Interscience
  Correspondence: tlowary@ualberta.ca
  Institutions: Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB, Canada
  
   
  
  Hafnia alvei 10457
  CSDB ID 24203 (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_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_1391962,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_143794,IEDB_150899,IEDB_151531,IEDB_153216,IEDB_153510,IEDB_190606,IEDB_423153,SB_137,SB_165,SB_166,SB_187,SB_195,SB_29,SB_7,SB_88

• Article ID: 4328
  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
  
   
  
  Acinetobacter calcoaceticus 7
  CSDB ID 27741 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_1391963,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_143260,IEDB_153207,IEDB_153216,IEDB_190606,IEDB_885822,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_88

• Article ID: 4328
  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 mimicus N-1990
  CSDB ID 27790 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Trivial name: type K82 CPS
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_141807,IEDB_147450,IEDB_150899,IEDB_151531,IEDB_153216,IEDB_190606,SB_137,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_29,SB_7,SB_8,SB_88

• Article ID: 5165
  Kasimova AA, Kenyon JJ, Arbatsky NP, Shashkov AS, Popova AV, Knirel YA, Hall RM "Structure of the K82 capsular polysaccharide of Acinetobacter baumannii LUH5534 containing a D-galactose 4,6-pyruvic acid acetal" - Biochemistry (Moscow) 83(7) (2018) 831-835
  

  Type K82 capsular polysaccharide (CPS) was isolated from Acinetobacter baumannii LUH5534. The structure of a linear tetrasaccharide repeating unit of the CPS was established by sugar analysis along with one- and two-dimensional 1H and 13C NMR spectroscopy. Proteins encoded by the KL82 capsule gene cluster in the genome of LUH5534 were assigned to roles in the synthesis of the K82 CPS. In particular, functions were assigned to two new glycosyltransferases (Gtr152 and Gtr153) and a novel pyruvyltransferase, Ptr5, responsible for the synthesis of d-galactose 4,6-(R)-pyruvic acid acetal.

  Acinetobacter baumannii, capsular polysaccharide structure, biotechnology, Pyruvic acid acetal, K locus, genetics of capsule biosynthesis

  NCBI PubMed ID: 30200867
  Publication DOI: 10.1134/S0006297918070064
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: yknirel@gmail.com; nastia-kasimova979797@mail.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia, School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700, Russia, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, GPC, dialysis, bioinformatic analysis (BLASTp)
  
   
  
  Acinetobacter baumannii LUH5534
  CSDB ID 12918 (all data & tools)
• Article ID: 5791
  Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" - Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
  

  Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.

  polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component

  Publication DOI: 10.1016/B978-0-12-819475-1.00005-5
  Publisher: Elsevier
  Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
  Editors: Barchi J, Kamerling H
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
  
   
  
  Acinetobacter baumannii K82 LUH5534
  CSDB ID 6739 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Trivial name: type K82 CPS
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_141807,IEDB_147450,IEDB_150899,IEDB_151531,IEDB_153216,IEDB_190606,SB_137,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_29,SB_7,SB_8,SB_88

• Article ID: 5165
  Kasimova AA, Kenyon JJ, Arbatsky NP, Shashkov AS, Popova AV, Knirel YA, Hall RM "Structure of the K82 capsular polysaccharide of Acinetobacter baumannii LUH5534 containing a D-galactose 4,6-pyruvic acid acetal" - Biochemistry (Moscow) 83(7) (2018) 831-835
  

  Type K82 capsular polysaccharide (CPS) was isolated from Acinetobacter baumannii LUH5534. The structure of a linear tetrasaccharide repeating unit of the CPS was established by sugar analysis along with one- and two-dimensional 1H and 13C NMR spectroscopy. Proteins encoded by the KL82 capsule gene cluster in the genome of LUH5534 were assigned to roles in the synthesis of the K82 CPS. In particular, functions were assigned to two new glycosyltransferases (Gtr152 and Gtr153) and a novel pyruvyltransferase, Ptr5, responsible for the synthesis of d-galactose 4,6-(R)-pyruvic acid acetal.

  Acinetobacter baumannii, capsular polysaccharide structure, biotechnology, Pyruvic acid acetal, K locus, genetics of capsule biosynthesis

  NCBI PubMed ID: 30200867
  Publication DOI: 10.1134/S0006297918070064
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: yknirel@gmail.com; nastia-kasimova979797@mail.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia, School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700, Russia, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, GPC, dialysis, bioinformatic analysis (BLASTp)
  
   
  
  Acinetobacter baumannii LUH5534
  CSDB ID 12620 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130646,IEDB_130648,IEDB_130697,IEDB_134627,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_137776,IEDB_140108,IEDB_140122,IEDB_141794,IEDB_141807,IEDB_147450,IEDB_151531,IEDB_153216,IEDB_190606,SB_165,SB_166,SB_173,SB_187,SB_195,SB_23,SB_24,SB_30,SB_7,SB_8,SB_88

• Article ID: 5211
  Senchenkova SN, Hou W, Naumenko OI, Geng P, Shashkov AS, Perepelov AV, Yang B, Knirel YA "Structure and genetics of a glycerol 2-phosphate-containing O-specific polysaccharide of Escherichia coli O33" - Carbohydrate Research 460 (2018) 47-50
  

  An O-specific polysaccharide was isolated by mild acid degradation of the lipopolysaccharide of Escherichia coli O33 followed by gel-permeation chromatography on Sephadex G-50. The polysaccharide was found to contain glycerol 2-phosphate (Gro-2-P), and the following structure of its tetrasaccharide repeat was established by sugar analysis, dephosphorylation, and 1D and 2D 1H and 13C NMR spectroscopy: The O33-antigen gene cluster was analyzed and found to be essentially consistent with the O-polysaccharide structure.

  Lipopolysaccharide, O-antigen, Escherichia coli, O-specific polysaccharide, bacterial polysaccharide structure, O-antigen gene cluster, glycerol phosphate

  NCBI PubMed ID: 29524726
  Publication DOI: 10.1016/j.carres.2018.02.008
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: andreivperepelov@gmail.com
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, School of Basic Medical Sciences, Tianjin Medical University, Heping District, Tianjin, 300070, PR China, Higher Chemical College of the Russian Academy of Sciences, D.I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, 31P NMR, GLC, mild acid hydrolysis, GPC, HF treatment, function analysis of gene clusters
  
   
  
  Escherichia coli O33 SSI E40
  CSDB ID 12975 (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 anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Escherichia coli O33
  CSDB ID 1401 (all data & tools)
• Article ID: 5472
  Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G "Structure and genetics of Escherichia coli O antigens" - FEMS Microbiology Reviews 44(6) (2020) 655-683
  

  Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and four (O14, O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.

  structure, O antigen, Escherichia coli, gene cluster, serogroup, diversity

  NCBI PubMed ID: 31778182
  Publication DOI: 10.1093/femsre/fuz028
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: G. Widmalm ; Lei Wang
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China, School of Molecular and Microbial Bioscience (G08), University of Sydney, Sydney, Australia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
  
   
  
  Escherichia coli O33
  CSDB ID 1541 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130646,IEDB_130648,IEDB_130697,IEDB_134627,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_137776,IEDB_140108,IEDB_140122,IEDB_141794,IEDB_141807,IEDB_147450,IEDB_151531,IEDB_153216,IEDB_190606,SB_165,SB_166,SB_173,SB_187,SB_195,SB_23,SB_24,SB_30,SB_7,SB_8,SB_88

• Article ID: 5211
  Senchenkova SN, Hou W, Naumenko OI, Geng P, Shashkov AS, Perepelov AV, Yang B, Knirel YA "Structure and genetics of a glycerol 2-phosphate-containing O-specific polysaccharide of Escherichia coli O33" - Carbohydrate Research 460 (2018) 47-50
  

  An O-specific polysaccharide was isolated by mild acid degradation of the lipopolysaccharide of Escherichia coli O33 followed by gel-permeation chromatography on Sephadex G-50. The polysaccharide was found to contain glycerol 2-phosphate (Gro-2-P), and the following structure of its tetrasaccharide repeat was established by sugar analysis, dephosphorylation, and 1D and 2D 1H and 13C NMR spectroscopy: The O33-antigen gene cluster was analyzed and found to be essentially consistent with the O-polysaccharide structure.

  Lipopolysaccharide, O-antigen, Escherichia coli, O-specific polysaccharide, bacterial polysaccharide structure, O-antigen gene cluster, glycerol phosphate

  NCBI PubMed ID: 29524726
  Publication DOI: 10.1016/j.carres.2018.02.008
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: andreivperepelov@gmail.com
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, School of Basic Medical Sciences, Tianjin Medical University, Heping District, Tianjin, 300070, PR China, Higher Chemical College of the Russian Academy of Sciences, D.I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, 31P NMR, GLC, mild acid hydrolysis, GPC, HF treatment, function analysis of gene clusters
  
   
  
  Escherichia coli O33 SSI E40
  CSDB ID 12781 (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 anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Escherichia coli O33
  CSDB ID 1402 (all data & tools)