CSDB: Search results

References to other databases: GTC:G88341KM, GlycomeDB:3558
Structural formula & atomic coordinates
Sweet-II 3D model
Show glycosyltransferases

Structures for the N-acetylneuraminic acid (Neu5Ac)-containing O56 and O24 polysaccharides of Escherichia coli have been reported previously. During these studies unusual chemical shifts had been observed for the NMR signals for H-3eq and C-3 of the Neu5Ac residues of both polysaccharides. In further pursuing this phenomenon, we have reinvestigated the O56 and O24 polysaccharides as well as derived oligosaccharides by one- and two-dimensional NMR spectroscopy. The results showed that structures of both polysaccharides (PSs) had to be modified and formulated as [formula: see text] 2D ROESY spectra revealed a strong NOE between H-3eq of Neu5Ac and the protons of the side-chain sugar (H-3 and H-5 of α-D-Galp in the O56 PS and H-3 of α-D-Glcp in the O24 PS) and also between H-3ax of Neu5Ac and H-3 of β-D-Glcp in the main chain. This indicated a close spatial association of the seven-linked α-Neu5Ac and the side-chain residues α-D-Galp (O56 PS) and α-D-Glcp (O25 PS), respectively. The strong long-range spatial contacts caused the unusual chemical shifts of H-3eq and C-3 of Neu5Ac.

Escherichia coli, NMR spectroscopy, polysaccharide structure, 024 and 056 antigens

NCBI PubMed ID: 7544238
Publication DOI: 10.1016/0008-6215(95)00041-Q
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: torgov@ioc.ac.ru
Institutions: Max-Planck-Institut für Immunbiologie, Freiburg, Germany
Methods: NMR-2D, NMR, sugar analysis, Smith degradation

No abstract available

Publication DOI: 10.1016/0008-6215(93)87026-O
Journal NLM ID: 0043535
Publisher: Elsevier
Institutions: Max-Planck-Institut für Immunbiologie, D-7800 Freiburg-Zähringen Germany
Methods: 13C NMR

O-antigen is part of the lipopolysaccharide present in the outer membrane of Gram-negative bacteria. It has many different forms, which are almost entirely due to genetic variations of O antigen gene clusters. In this study, the O antigen gene clusters of E. coli O24 and O56 were sequenced, and all genes were assigned functions on the basis of homology. Comparison of O antigen gene clusters indicated that E. coli O24 O antigen gene cluster has possibly arisen from the E. coli O56 gene cluster, through inactivation of two glycosyltransferase genes and acquisition of two new genes from E. coli O157 and O152, respectively. The insertion sequence elements seemed to play important roles for the assembly of the O24 O antigen gene cluster. This is the first time that the evolutionary history of a multi-origin O antigen gene cluster is clearly demonstrated. Genes specific to E. coli O24 and O56 were also identified, which may be used for development of DNA-based serotyping schemes.

Lipopolysaccharide, O-antigen, gene cluster, glycosyltransferase, serotyping, biotechnology, outer membrane

NCBI PubMed ID: 17072668
Publication DOI: 10.1007/s00284-006-0032-7
Journal NLM ID: 7808448
Publisher: Springer International
Correspondence: fenglu63@nankai.edu.cn
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 HongDa Street, Tianjin, TEDA, 300457, P.R. China
Methods: genetic methods

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 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