Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_144990,IEDB_147450,IEDB_150767,IEDB_150948,IEDB_151528,IEDB_152214,IEDB_153553,IEDB_167071,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461719,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_25,SB_7,SB_8,SB_86,SB_88

• Article ID: 266
  Inamori K, Saito T, Iwaki D, Nagira T, Iwanaga S, Arisaka F, Kawabata S "A newly identified horseshoe crab lectin with specificity for blood group A antigen recognizes specific O-antigens of bacterial lipopolysaccharides" - Journal of Biological Chemistry 274(6) (1999) 3272-3278
  

  14-kDa lectin, named tachylectin-3, was newly identified from hemocytes of the Japanese horseshoe crab, Tachypleus tridentatus. This lectin exhibited hemagglutinating activity against human A-type erythrocytes, but not against the B- and O-types of erythrocytes and animal erythrocytes, including those of sheep, rabbit, horse, and bovine. The hemagglutinating activity of tachylectin-3 was equivalent to that of a previously identified lectin, named tachylectin-2, with affinity for N-acetyl-D-glucosamine or N-acetyl-D-galactosamine. However, the activity of tachylectin-3 was not inhibited by these two N-acetylhexosamines at 100 mM but was inhibited by a blood group A-pentasaccharide at a minimum inhibitory concentration of 0.16 mM. Furthermore, the hemagglutinating activity was strongly inhibited by bacterial S-type lipopolysaccharides (LPSs) from Gram-negative bacteria but not by R-type LPSs lacking O-antigens. One of the most effective S-type LPSs was from Escherichia coli O111:B4, with a minimum inhibitory concentration of 6 ng/ml. These data suggest that tachylectin-3 specifically recognizes Gram-negative bacteria through the unique structural units of O-antigens. Ultracentrifugation analysis revealed that tachylectin-3 is present in dimer in solution. A cDNA coding for tachylectin-3 was isolated from a hemocyte cDNA library. Tachylectin-3 consisted of two repeating sequences, each with a partial sequence similarity to rinderpest virus neuraminidase. Tachylectin-3 and three previously isolated types of tachylectins were all predominantly expressed in hemocytes and released from hemocytes in response to external stimuli. These lectins present at injured sites suggest that they probably serve synergistically to accomplish an effective host defense against invading microbes.

  antigen, lipopolysaccharides, O-antigen, specificity, blood group A, lectin

  NCBI PubMed ID: 9920866
  Publication DOI: 10.1074/jbc.274.6.3272
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: skawascb@mbox.nc.kyushu-u.ac.jp
  Institutions: Departments of Molecular Biology, Graduate School of Medical Science and Biology, Faculty of Science, Kyushu University, Fukuoka 812-8581, Department of Life Science, Faculty of Bioscience and Bioengineering, Tokyo Institute of Technology, Yokohama 226-8501, Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Tokyo 101-0062, Japan., Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Tokyo 101-0062, Japan
  
   
  
  Escherichia coli O128
  CSDB ID 7240 (all data & tools)
• Article ID: 371
  Sengupta P, Bhattacharyya T, Majumder M, Chatterjee BP "Determination of the immunodominant part in the O-antigenic polysaccharide from Escherichia coli O128 by ELISA-inhibition study" - FEMS Immunology and Medical Microbiology 28(2) (2000) 133-137
  

  The immunodominant part in the O-antigenic polysaccharide from Escherichia coli O128 was immunologically characterized by an enzyme‐linked immunosorbent assay (ELISA). The antibody specificity was determined by the inhibitory effects of the methyl glycosides of constituent mono‐ and oligosaccharides synthesized related to the O-antigenic polysaccharide from E. coli O128. It was found that methyl α-L-fucopyranoside was the most effective inhibitor amongst the monosaccharides while the highest antibody specificity was directed towards the trisaccharide with the structure: β-D-GalpNAc-(1→6)-[α-L-Fuc-(1→2)-β-D-Galp-1→OMe suggesting that the monospecific antibody has the extended combining site.

  Lipopolysaccharide, O-antigenic polysaccharide, Escherichia coli O128, immunodominant, monospecific IgG

  NCBI PubMed ID: 10799803
  Publication DOI: 10.1111/j.1574-695X.2000.tb01467.x
  Journal NLM ID: 9315554
  Publisher: Elsevier
  Correspondence: bcbpc@mahendra.iacs.res.in
  Institutions: Department of Biological Chemistry, Indian Association for the Cultivation of Sciences, Calcutta, India
  Methods: immunochemical methods
  
   
  
  Escherichia coli O128
  CSDB ID 8302 (all data & tools)
• Article ID: 1200
  Sengupta P, Bhattacharyya T, Shashkov AS, Kochanowski H, Basu S "Structure of the O-specific side chain of the Escherichia coli O128 lipopolysaccharide" - Carbohydrate Research 277 (1995) 283-290
  

  Lipopolysaccharide, NMR, LPS, structure, chain, side chain, Escherichia, Escherichia coli, O-specific, Escherichia coli O128

  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Biological Chemistry, Indian Association for the Cultivation of Sciences, Calcutta, India
  Methods: NMR
  
   
  
  Escherichia coli O128
  CSDB ID 4646 (all data & tools)
• Article ID: 3196
  Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" - FEMS Microbiology Reviews 30(3) (2006) 382-403
  

  Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/

  NMR, structure, serotype, O-antigen, Enterobacteriacea, database

  NCBI PubMed ID: 16594963
  Publication DOI: 10.1111/j.1574-6976.2006.00016.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: andrej.weintraub@ki.se
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  
   
  
  Escherichia coli O128
  CSDB ID 20681 (all data & tools)
• Article ID: 3430
  Ali T, Weintraub A, Widmalm G "Structural studies of the O-antigenic polysaccharides from the enteroaggregative Escherichia coli strain 87/D2 and international type strains from E. coli O128" - Carbohydrate Research 343(4) (2008) 695-702
  

  The O-antigen of the lipopolysaccharide (LPS) from the enteroaggregative Escherichia coli strain 87/D2 has been determined by component analysis together with NMR spectroscopy. The polysaccharide has pentasaccharide repeating units in which all the residues have the galacto-configuration. The repeating unit of the O-antigen, elucidated using the O-deacylated LPS, is branched with the following structure: Analysis of the (1)H NMR spectrum of the LPS revealed O-acetyl groups (approximately 0.7 per repeating unit) distributed over two positions. Subsequent analysis showed that the galactose residue carries acetyl groups at either O-3 or O-4 in a ratio of approximately 2:1. The international reference strain from E. coli O128ab was investigated and the repeating unit of the O-antigens has the following structure: Analysis of the (1)H NMR spectrum of the LPS revealed O-acetyl groups (approximately one per repeating unit) distributed over two positions. The integrals of the resonances for the O-acetyl groups indicated similarities between the O-antigen from E. coli O128ab and that of E. coli strain 87/D2, whereas the O-acetyl substitution pattern in the E. coli O128ac O-antigen differed slightly. Enzyme immunoassay using specific anti-E. coli O128ab and anti-E. coli O128ac rabbit sera confirmed the results

  Lipopolysaccharide, NMR, Escherichia coli, serology, biological repeating unit, Enteroaggregative

  NCBI PubMed ID: 18237721
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Karolinska Institute, Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, alkaline degradation, NMR-1D, immunochemical methods
  
   
  
  Escherichia coli O128ab
  CSDB ID 22801 (all data & tools)
• Article ID: 3503
  Li M, Liu XW, Shao J, Shen J, Jia Q, Yi W, Song JK, Woodward R, Chow CS, Wang PG "Characterization of a Novel a1,2-Fucosyltransferase of Escherichia coli O128:B12 and Functional Investigation of Its Common Motif" - Biochemistry 47(1) (2008) 378-387
  

  The wbsJ gene from Escherichia coli O128:B12 encodes an α1,2-fucosyltransferase responsible for adding a fucose onto the galactose residue of the O-antigen repeating unit via an α1,2 linkage. The wbsJ gene was overexpressed in E. coli BL21 (DE3) as a fusion protein with glutathione S-transferase (GST) at its N-terminus. GST-WbsJ fusion protein was purified to homogeneity via GST affinity chromatography followed by size exclusion chromatography. The enzyme showed broad acceptor specificity with Galβ1,3GalNAc (T antigen), Galβ1,4Man and Galβ1,4Glc (lactose) being better acceptors than Galβ-O-Me and galactose. Galβ1,4Fru (lactulose), a natural sugar, was furthermore found to be the best acceptor for GST-WbsJ with a reaction rate four times faster than that of lactose. Kinetic studies showed that GST-WbsJ has a higher affinity for lactose than lactulose with apparent Km values of 7.81 mM and 13.26 mM, respectively. However, the kcat/appKm value of lactose (6.36 M-1.min-1) is two times lower than that of lactulose (13.39 M-1.min-1). In addition, the α1,2-fucosyltransferase activity of GST-WbsJ was found to be independent of divalent metal ions such as Mn2+ or Mg2+. This activity was competitively inhibited by GDP with a Ki value of 1.41 mM. Site-directed mutagenesis and a GDP-bead binding assay were also performed to investigate the functions of the highly conserved motif H152xR154R155xD157. In contrast to α1,6-fucosyltransferases, none of the mutants of WbsJ within this motif exhibited a complete loss of enzyme activity. However, residues R154 and D157 were found to play critical roles in donor binding and enzyme activity. The results suggest that the common motif shared by both α1,2-fucosyltransferases and α1,6-fucosyltransferases have similar functions. Enzymatic synthesis of fucosylated sugars in milligram scale was successfully performed using Galβ-O-Me and Galβ1,4Glcβ-N3 as acceptors

  O-antigen, Escherichia coli, enzymatic synthesis, a-1, 2-fucosyltransferase, wbsJ gene

  NCBI PubMed ID: 18078329
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Correspondence: wang.892@osu.edu
  Institutions: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Biochemistry and Chemistry, The Ohio State University, Columbus, Ohio 43210
  Methods: 13C NMR, 1H NMR, ESI-MS, NMR-1D, genetic methods, biochemical methods
  
   
  
  Escherichia coli O128:B12
  CSDB ID 22685 (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 O128ab, Escherichia coli O128ac
  CSDB ID 1867 (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_130701,IEDB_134627,IEDB_136044,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_137485,IEDB_1391961,IEDB_1391963,IEDB_141584,IEDB_141794,IEDB_142489,IEDB_143260,IEDB_144562,IEDB_144983,IEDB_144990,IEDB_147450,IEDB_150766,IEDB_150767,IEDB_150948,IEDB_151528,IEDB_152206,IEDB_152214,IEDB_152215,IEDB_153553,IEDB_167071,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461710,IEDB_461711,IEDB_461719,IEDB_885822,IEDB_983930,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_44,SB_67,SB_7,SB_72,SB_8,SB_86,SB_88

• Article ID: 2681
  Ovodov YS, Gorshkova RP, Tomshich SV, Komandrova NA, Zubkov VA, Kalmykova EN, Isakov VV "Chemical and Immunochemical studies on lipopolysaccharides of some Yersinia species - A review of some recent investigations" - Journal of Carbohydrate Chemistry 11 (1992) 21-35
  

  The present paper revealed the results of some recent chemical and immunochemical studies of the lipopolysaccharides from various species and erologie variants of Yersinia genus as follows: Y. pseudotuberculosis IIC and VII; Y. enterocolitica 0:1, 2a, 3; 0:2a, 2b, 3; 0:3; 0:4, 32; 0:5; 0:5,27; 0:6,31; 0:7,8; 0:19,8; 0:8; Y. frederiksenii 0:16,29; Y. intermedia 0:4,33; Y. aldovae.

  Publication DOI: 10.1080/07328309208016139
  Journal NLM ID: 8218151
  Publisher: Marcel Dekker
  Institutions: The Pacific Institute of Bioorganic Chemistry, Far East Branch of the USSR Academy of Sciences, 690022, Vladivostok, U.S.S.R
  Methods: 13C NMR, 1H NMR
  
   
  
  Yersinia enterocolitica O19,8, Yersinia enterocolitica O7,8
  CSDB ID 137835 (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_134627,IEDB_136044,IEDB_136045,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141501,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_147450,IEDB_150767,IEDB_150948,IEDB_152214,IEDB_153207,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461719,IEDB_885822,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_86,SB_88

• Article ID: 3430
  Ali T, Weintraub A, Widmalm G "Structural studies of the O-antigenic polysaccharides from the enteroaggregative Escherichia coli strain 87/D2 and international type strains from E. coli O128" - Carbohydrate Research 343(4) (2008) 695-702
  

  The O-antigen of the lipopolysaccharide (LPS) from the enteroaggregative Escherichia coli strain 87/D2 has been determined by component analysis together with NMR spectroscopy. The polysaccharide has pentasaccharide repeating units in which all the residues have the galacto-configuration. The repeating unit of the O-antigen, elucidated using the O-deacylated LPS, is branched with the following structure: Analysis of the (1)H NMR spectrum of the LPS revealed O-acetyl groups (approximately 0.7 per repeating unit) distributed over two positions. Subsequent analysis showed that the galactose residue carries acetyl groups at either O-3 or O-4 in a ratio of approximately 2:1. The international reference strain from E. coli O128ab was investigated and the repeating unit of the O-antigens has the following structure: Analysis of the (1)H NMR spectrum of the LPS revealed O-acetyl groups (approximately one per repeating unit) distributed over two positions. The integrals of the resonances for the O-acetyl groups indicated similarities between the O-antigen from E. coli O128ab and that of E. coli strain 87/D2, whereas the O-acetyl substitution pattern in the E. coli O128ac O-antigen differed slightly. Enzyme immunoassay using specific anti-E. coli O128ab and anti-E. coli O128ac rabbit sera confirmed the results

  Lipopolysaccharide, NMR, Escherichia coli, serology, biological repeating unit, Enteroaggregative

  NCBI PubMed ID: 18237721
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Karolinska Institute, Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, alkaline degradation, NMR-1D, immunochemical methods
  
   
  
  Escherichia coli 87/D2
  CSDB ID 22601 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: repeating O-unit
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_144990,IEDB_147450,IEDB_150767,IEDB_150948,IEDB_151528,IEDB_152214,IEDB_152215,IEDB_153553,IEDB_167071,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461719,IEDB_885822,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_25,SB_7,SB_8,SB_86,SB_88

• Article ID: 3892
  Lundborg M, Modhukur V, Widmalm G "Glycosyltransferase functions of E. coli O-antigens" - Glycobiology 20(3) (2010) 366-368
  

  ECODAB (the E. coli O-antigen database) has been expanded to include information about glycosyltransferases (GTs) involved in the assembly of the O-antigen polysaccharide. Similarity searches have been performed to be able to determine GT functions that have not been reported prior to this work. In addition to suggesting the function of 179 GTs the approach leads to the prediction of part of the O-antigen structures of a number of serogroups. The procedure suggests a novel way of combining genetic information with experimental techniques in structural analysis of oligo- and polysaccharides.

  O-antigen, polysaccharides, Escherichia coli, glycosyltransferases, database

  NCBI PubMed ID: 19926726
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  Methods: genetic methods
  
   
  
  Escherichia coli O128
  CSDB ID 25334 (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_134627,IEDB_136044,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_144990,IEDB_147450,IEDB_150767,IEDB_150948,IEDB_151528,IEDB_152214,IEDB_153553,IEDB_167071,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461719,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_25,SB_7,SB_8,SB_86,SB_88

• Article ID: 4067
  Lundborg M, Widmalm G "Structural analysis of glycans by NMR chemical shift prediction" - Analytical Chemistry 83(5) (2011) 1514-1517
  

  Structural determination of N- and O-linked glycans as well as polysaccharides is hampered by the limited spectral dispersion. The computerized approach CASPER, an acronym for computer assisted spectrum evaluation of regular polysaccharides, uses liquid state NMR data to elucidate carbohydrate structure based on agreement with predicted (1)H and (13)C chemical shifts. We here demonstrate developments based on multiple through-bond J-based correlations that significantly enhance the credence to the sequence connectivities proposed in the analysis exemplified by an oligosaccharide and a bacterial polysaccharide. The approach is also suitable for predicting (1)H and (13)C NMR chemical shifts of synthesized oligosaccharides and glycoconjugates, thereby corroborating a proposed structure.

  NMR, CASPER, N-linked glycan, O-linked glycan

  NCBI PubMed ID: 21280662
  Journal NLM ID: 0370536
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, NMR-2D, NMR-1D, computer analysis with CASPER
  
   
  
  Escherichia coli O128
  CSDB ID 26277 (all data & tools)
• Article ID: 5532
  Zheng H, Naumenko OI, Wang H, Xiong Y, Wang J, Shashkov AS, Li Q, Knirel YA "Colitose-containing O-polysaccharide structure and O-antigen gene cluster of Escherichia albertii HK18069 related to those of Escherichia coli O55 and E.coli O128" - Carbohydrate Research 480 (2019) 73-79
  

  A 3,6-dideoxy-l-xylo-hexose (colitose)-containing partially O-acetylated branched polysaccharide was obtained by mild acid hydrolysis (2% HOAc, 100 �C, 2 h) of the lipopolysaccharide of Escherichia albertii HK18069 followed by gel-permeation chromatography on Sephadex G-50 Superfine. Part of colitose residues (~40%) was cleaved upon hydrolysis, and the full cleavage was achieved by prolonged hydrolysis (8 h) under the same conditions and resulted in a modified linear polysaccharide. Structure of the O-polysaccharide of E. albertii HK18069 was established by 1D and 2D 1H and 13C NMR spectroscopy applied to both initial and modified O-deacetylated and colitose-free polysaccharides: [structure: see text] where β-d-Galp is mono-O-acetylated at position either 3 (~50%) or 4 (~30%). The O-antigen gene cluster of E. albertii HK18069 between conserved galF and gnd genes together with flanking regions was sequenced, and predicted functions of the genes were found to be consistent with the O-polysaccharide structure established. The O-polysaccharide structure and the O-antigen gene cluster of E. albertii HK18069 are related to those of Esherichia coli O55 and E. coli O128 reported earlier. It is proposed to create for strain HK18069 a new E. albertii O-serogroup, O8.

  Escherichia coli, O-specific polysaccharide, O-acetylation, bacterial polysaccharide structure, O-antigen gene cluster, colitose, Escherichia albertii

  Publication DOI: 10.1016/j.carres.2019.05.013
  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, Zigong Center for Disease Control and Prevention, Zigong, Sichuan Province, China, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, de-O-acetylation, GPC, bioinformatics analysis
  
   
  
  Escherichia coli O128
  CSDB ID 2367 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_147450,IEDB_150767,IEDB_150948,IEDB_151531,IEDB_152214,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_423141,IEDB_461711,IEDB_461719,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_86,SB_88

• Article ID: 4690
  Knirel YA, Gabius H, Blixt O, Rapoport EM, Khasbiullina NR, Shilova NV, Bovin NV "Human tandem-repeat-type galectins bind bacterial non-bGal polysaccharides" - Glycoconjugate Journal 31(1) (2014) 7-12
  

  Galectins are multifunctional effectors, for example acting as regulators of cell growth via protein-glycan interactions. The observation of capacity to kill bacteria for two tandem-repeat-type galectins, which target histo-blood epitopes toward this end (Stowell et al. Nat. Med. 16:295-301, 2010), prompted us to establish an array with bacterial polysaccharides. We addressed the question whether sugar determinants other than ?-galactosides may be docking sites, using human galectins-4, -8, and -9. Positive controls with histo-blood group ABH-epitopes and the E. coli 086 polysaccharide ascertained the suitability of the set-up. Significant signal generation, depending on type of galectin and polysacchride, was obtained. Presence of cognate ?-galactoside-related epitopes within a polysaccharide chain or its branch will not automatically establish binding properties, and structural constellations lacking galactosides, like rhamnan, were found to be active. These data establish the array as valuable screening tool, giving direction to further functional and structural studies.

  glycan, Bacterial polysaccharide, ABO, galectin, printed glycan array, rhamnoside

  NCBI PubMed ID: 24065176
  Publication DOI: 10.1007/s10719-013-9497-3
  Journal NLM ID: 8603310
  WWW link: doi:10.1007/s10719-013-9497-3
  Publisher: Kluwer Academic Publishers
  Correspondence: bovin@carb.ibch.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp., 47, Moscow, Russian Federation, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10
  Methods: GPC, mild acid degradation, binding assays
  
   
  
  Salmonella enterica O13
  CSDB ID 30309 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_136045,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141501,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_147450,IEDB_150767,IEDB_150948,IEDB_152214,IEDB_153207,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461719,IEDB_885822,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_86,SB_88

• 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 O128ac 87/D2
  CSDB ID 1868 (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_134627,IEDB_136044,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_144990,IEDB_147450,IEDB_150767,IEDB_150948,IEDB_151528,IEDB_152214,IEDB_153553,IEDB_167071,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461719,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_25,SB_7,SB_8,SB_86,SB_88

• Article ID: 5481
  Naumenko OI, Senchenkova SN, Knirel YA "O-Specific polysaccharides of a new species of enteric bacteria Escherichia albertii closely related to E. coli" - Russian Journal of Bioorganic Chemistry 45(6) (2019) 451-462
  

  The data on the structure of O-specific polysaccharides (O-antigens) of all nine known molecular types (potential O-serotypes) of a new type of enterobacteria Escherichia albertii, causative agents of intestinal infections in humans and birds, are presented. The advantages and limitations of structural analysis methods used to determine the structure of E. albertii polysaccharides are discussed. The annotation of genes in gene clusters of biosynthesis of O-antigens of E. albertii was carried out by comparison with the sequences in the available databases. Structural and genetic relationships between O-antigens of E. albertii and closely related species of E. coli are discussed. It was found that, in addition to the O-antigen, E. albertii O9 expresses a mannan of the same structure as the mannan of E. coli O8.

  biosynthesis, structure, O-antigen, Escherichia coli, O-specific polysaccharide, glycosyltransferase, O-antigen gene cluster, selective cleavage, glycosidic bond, Escherichia albertii, bacterial mannan

  Publication DOI: 10.1134/S1068162019060293
  Journal NLM ID: 9420101
  Publisher: Springer Science and Business Media
  Correspondence: YA Knirel
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: solvolysis with CF3CO2H, acid hydrolysis with CF3CO2H
  
   
  
  Escherichia coli O128
  CSDB ID 2217 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_134627,IEDB_136044,IEDB_136045,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141501,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_147450,IEDB_150767,IEDB_150948,IEDB_152214,IEDB_153207,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461719,IEDB_885822,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_86,SB_88

• Article ID: 5532
  Zheng H, Naumenko OI, Wang H, Xiong Y, Wang J, Shashkov AS, Li Q, Knirel YA "Colitose-containing O-polysaccharide structure and O-antigen gene cluster of Escherichia albertii HK18069 related to those of Escherichia coli O55 and E.coli O128" - Carbohydrate Research 480 (2019) 73-79
  

  A 3,6-dideoxy-l-xylo-hexose (colitose)-containing partially O-acetylated branched polysaccharide was obtained by mild acid hydrolysis (2% HOAc, 100 �C, 2 h) of the lipopolysaccharide of Escherichia albertii HK18069 followed by gel-permeation chromatography on Sephadex G-50 Superfine. Part of colitose residues (~40%) was cleaved upon hydrolysis, and the full cleavage was achieved by prolonged hydrolysis (8 h) under the same conditions and resulted in a modified linear polysaccharide. Structure of the O-polysaccharide of E. albertii HK18069 was established by 1D and 2D 1H and 13C NMR spectroscopy applied to both initial and modified O-deacetylated and colitose-free polysaccharides: [structure: see text] where β-d-Galp is mono-O-acetylated at position either 3 (~50%) or 4 (~30%). The O-antigen gene cluster of E. albertii HK18069 between conserved galF and gnd genes together with flanking regions was sequenced, and predicted functions of the genes were found to be consistent with the O-polysaccharide structure established. The O-polysaccharide structure and the O-antigen gene cluster of E. albertii HK18069 are related to those of Esherichia coli O55 and E. coli O128 reported earlier. It is proposed to create for strain HK18069 a new E. albertii O-serogroup, O8.

  Escherichia coli, O-specific polysaccharide, O-acetylation, bacterial polysaccharide structure, O-antigen gene cluster, colitose, Escherichia albertii

  Publication DOI: 10.1016/j.carres.2019.05.013
  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, Zigong Center for Disease Control and Prevention, Zigong, Sichuan Province, China, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, de-O-acetylation, GPC, bioinformatics analysis
  
   
  
  Escherichia coli O128ab (87/D2)
  CSDB ID 2368 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Contained glycoepitopes: IEDB_115013,IEDB_130645,IEDB_130648,IEDB_134627,IEDB_136044,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_140125,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_147450,IEDB_149558,IEDB_150767,IEDB_150945,IEDB_150948,IEDB_151528,IEDB_152212,IEDB_152214,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461717,IEDB_461719,IEDB_918314,SB_148,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_86,SB_87,SB_88

• 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
  
   
  
  Escherichia coli O86:B7
  CSDB ID 3832 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Aglycon: core-lipid A
Contained glycoepitopes: IEDB_115013,IEDB_130645,IEDB_130648,IEDB_134627,IEDB_136044,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_140125,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_147450,IEDB_149558,IEDB_150767,IEDB_150945,IEDB_150948,IEDB_151528,IEDB_152212,IEDB_152214,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_241096,IEDB_461711,IEDB_461717,IEDB_461719,IEDB_918314,SB_148,SB_154,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_86,SB_87,SB_88

• 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
  
   
  
  Escherichia coli O86:B7
  CSDB ID 3637 (all data & tools)