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  • 1.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lundborg, Magnus
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rapid structural elucidation of polysaccharides employing predicted functions of glycosyltransferases and NMR data: Application to the O-antigen of Escherichia coli O592014In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 24, no 5, p. 450-457Article in journal (Refereed)
    Abstract [en]

    A computerized method that uses predicted functions of glycosyltransferases (GTs) in conjunction with unassigned NMR data has been developed for the structural elucidation of bacterial polysaccharides (PSs). In this approach, information about the action of GTs (consisting of possible sugar residues used as donors and/or acceptors, as well as the anomeric configuration and/or substitution position in the respective glycosidic linkages) is extracted from the Escherichia coli O-antigen database and is submitted, together with the unassigned NMR data, to the CASPER program. This time saving methodology, which alleviates the need for chemical analysis, was successfully implemented in the structural elucidation of the O-antigen PS of E. coli O59. The repeating unit of the O-specific chain was determined using the O-deacylated PS and has a branched structure, namely, -> 6)[alpha-d-GalpA3Ac/4Ac-(1 -> 3)]-alpha-d-Manp-(1 -> 3)-alpha-d-Manp-(1 -> 3)-beta-d-Manp-(1 -> 3)-alpha-d-GlcpNAc-(1 ->. The identification of the O-acetylation positions was efficiently performed by comparison of the H-1,C-13 HSQC NMR spectra of the O-deacylated lipopolysaccharide and the lipid-free PS in conjunction with chemical shift predictions made by the CASPER program. The side-chain d-GalpA residue carries one equivalent of O-acetyl groups at the O-3 and O-4 positions distributed in the LPS in a 3:7 ratio, respectively. The presence of O-acetyl groups in the repeating unit of the E. coli O59 PS is consistent with the previously proposed acetyltransferase WclD in the O-antigen gene cluster.

  • 2.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ramström, Kristoffer
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural studies of the O-antigen polysaccharide from Escherichia coli O115 and biosynthetic aspects thereof2013In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 23, no 3, p. 354-362Article in journal (Refereed)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) of Escherichia coliO115 has been investigated using a combination of component analysis and 1D and 2D nuclear magnetic resonance (NMR) spectroscopy experiments. The repeating unit of the O-antigen was elucidated using the O-deacetylated PS and has the following branched pentasaccharide structure: →3)[β-L-Rhap-(1 → 4)]-β-D-GlcpNAc-(1 → 4)-α-D-GalpA-(1 → 3)-α-D-Manp-(1 → 3)-β-D-GlcpNAc-(1→. Cross-peaks of low intensity, corresponding to a β-L-Rhap-(1 → 4)-β-D-GlcpNAc-(1→ structural element, were present in the NMR spectra and attributed to the terminal part of the PS; this information defines the biological repeating unit of the O-antigen by having a 3-substituted N-acetyl-D-glucosamine (GlcNAc) residue at its reducing end. Analysis of the NMR spectra of the native PS revealed O-acetyl groups distributed over different positions of theL-Rhap residue (∼0.70 per repeating unit) as well as at O-2 and O-3 of the D-GalpA residue (∼0.03 and ∼0.25 per repeating unit, respectively), which is in agreement with the presence of two acetyltransferases previously identified in the O-antigen gene cluster (Wang Q, Ruan X, Wei D, Hu Z, Wu L, Yu T, Feng L, Wang L. 2010. Mol Cell Probes. 24:286–290.). In addition, the four glycosyltransferases initially identified in the O-antigen gene cluster of E. coli O115 were analyzed using BLAST, and the function of two of them predicted on the basis of similarities with glycosyltransferases from Shigella dysenteriae type 5 and 12, as well as E. coli O58 and O152.

  • 3.
    Julenius, Karin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    NetCGlyc 1.0: prediction of mammalian C-mannosylation sites2007In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 17, no 8, p. 868-876Article in journal (Refereed)
    Abstract [en]

    C-mannosylation is the attachment of an alpha-mannopyranose to a tryptophan via a C-C linkage. The sequence WXXW, in which the first Trp becomes mannosylated, has been suggested as a consensus motif for the modification, but only two-thirds of known sites follow this rule. We have gathered a data set of 69 experimentally verified C-mannosylation sites from the literature. We analyzed these for sequence context and found that apart from Trp in position + 3, Cys is accepted in the same position. We also find a clear preference in position + 1, where a small and/or polar residue (Ser, Ala, Gly, and Thr) is preferred and a Phe or a Len residue discriminated against. The Protein Data Bank was searched for structural information, and five structures of C-mannosylated proteins were obtained. We showed that modified tryptophan residues are at least partly solvent exposed. A method predicting the location of C-mannosylation sites in proteins was developed using a neural network approach. The best overall network used a 21-residue sequence input window and information on the presence/ absence of the WXXW motif. NetCGlyc 1.0 correctly predicts 93% of both positive and negative C-mannosylation sites. This is a significant improvement over the WXXW consensus motif itself, which only identifies 67% of positive sites. NetCGlyc 1.0 is available at http://www.cbs.dtu.dk/ services/NetCGlyc/. Using NetCGlyc 1.0, we scanned the human genome and found 2573 exported or transmembrane transcripts with at least one predicted C-mannosylation site.

  • 4. Liu, Bin
    et al.
    Perepelov, Andrei V.
    Svensson, Mona V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Shevelev, Sergei D.
    Guo, Dan
    Senchenkova, Sof'ya N.
    Shashkov, Alexander S.
    Weintraub, Andrej
    Feng, Lu
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Knirel, Yuriy A.
    Wang, Lei
    Genetic and structural relationships of Salmonella O55 and Escherichia coli O103 O-antigens and identification of a 3-hydroxybutanoyltransferase gene involved in the synthesis of a Fuc3N derivative2010In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 20, no 6, p. 679-688Article in journal (Refereed)
    Abstract [en]

    O-antigen (O-polysaccharide), a part of the outer membrane of Gram-negative bacteria, is one of the most variable cell constituents and is related to bacterial virulence. O-antigen diversity is almost entirely due to genetic variations in O-antigen gene clusters. In this study, the O-polysaccharide structures of Salmonella O55 and Escherichia coli O103 were elucidated by chemical analysis and nuclear magnetic resonance spectroscopy. It was found that the O-polysaccharides have similar pentasaccharide O-units, which differ only in one sugar (glucose versus N-acetylglucosamine) and in the N-acyl group (acetyl versus 3-hydroxybutanoyl) on 3-amino-3,6-dideoxy-d-galactose (d-Fuc3N). The Salmonella O55 antigen gene cluster was sequenced and compared with the E. coli O103 antigen gene cluster reported previously. The two gene clusters were found to share high-level similarity (DNA identity ranges from 53% to 76%), except for two putative acyl transferase genes (fdtC in Salmonella O55 and fdhC in E. coli O103) which show no similarity. Replacement of the fdtC gene in Salmonella O55 with the fdhC gene from E. coli O103 resulted in production of a modified O-antigen, which contains a 3-hydroxybutanoyl derivative of Fuc3N in place of 3-acetamido-3,6-dideoxygalactose. This finding strongly suggests that fdhC is a 3-hydroxybutanoyltransferase gene. The sequence similarity level suggested that the O-antigen gene clusters of Salmonella O55 and E. coli O103 originate from a common ancestor, and this evolutionary relationship is discussed.

  • 5.
    Lundborg, Magnus
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Modhukur, Vijayachitra
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Glycosyltransferase functions of E. coli O-antigens2010In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 20, no 3, p. 366-368Article in journal (Refereed)
    Abstract [en]

    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.

  • 6. Rojas-Macias, Miguel A.
    et al.
    Ståhle, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Luetteke, Thomas
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Development of the ECODAB into a relational database for Escherichia coli O-antigens and other bacterial polysaccharides2015In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 25, no 3, p. 341-347Article in journal (Refereed)
    Abstract [en]

    Escherichia coli O-antigen database (ECODAB) is aweb-based application to support the collection of E. coli O-antigen structures, polymerase and flippase amino acid sequences, NMR chemical shift data of O-antigens as well as information on glycosyltransferases (GTs) involved in the assembly of O-antigen polysaccharides. The database content has been compiled from scientific literature. Furthermore, the system has evolved from being a repository to one that can be used for generating novel data on its own. GT specificity is suggested through sequence comparison with GTs whose function is known. The migration of ECODAB to a relational database has allowed the automation of all processes to update, retrieve and present information, thereby, endowing the system with greater flexibility and improved overall performance. ECODAB is freely available at http://www.casper.organ.su.se/ECODAB/. Currently, data on 169 E. coli unique O-antigen entries and 338 GTs is covered. Moreover, the scope of the database has been extended so that polysaccharide structure and related information from other bacteria subsequently can be added, for example, from Streptococcus pneumoniae.

  • 7. Senchenkova, Sof'ya N.
    et al.
    Zhang, Yuanyuan
    Perepelov, Andrei V.
    Guo, Xi
    Shashkov, Alexander S.
    Weintraub, Andrej
    Liu, Bin
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Knirel, Yuriy A.
    Structure and gene cluster of the O-antigen of Escherichia coli O165 containing 5-N-acetyl-7-N-[(R)-3-hydroxybutanoyl]pseudaminic acid2016In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 26, no 4, p. 335-342Article in journal (Refereed)
    Abstract [en]

    Upon mild acid degradation of the lipopolysaccharide of Escherichia coli O165, the O-polysaccharide chain was cleaved at the glycosidic linkage of 5-N-acetyl-7-N-[(R)-3-hydroxybutanoyl]pseudaminic acid (Pse5Hb7Ac). Analysis of the resulting linear tetrasaccharide and alkali-treated lipopolysaccharide by 1H/13C 1D and 2D nuclear magnetic resonance spectroscopy enabled elucidation of the following structure of the O-polysaccharide: →8)-α-Psep5Hb7Ac-(2 → 6)-β-D-Galp-(1 → 4)-β-D-Glсp-(1 → 3)-α-DGlсpNAc-(1→. The β-D-Galp-(1 → 4)-β-D-Glсp-(1 → 3)-D-GlсpNAc structural element is also present in the O-polysaccharide of E. coli O82. The content of the O-antigen gene cluster of E. coli O165 was found to be consistent with the O-polysaccharide structure established. Functions of proteins encoded in the gene cluster, including enzymes involved in the Pse5Hb7Ac biosynthesis and glycosyltransferases, were putatively assigned by comparison with sequences in available databases.

  • 8.
    Ståhle, Jonas
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Fontana, Carolina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Elucidation of the O-antigen structure of Escherichia coli O632019In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 29, no 2, p. 179-187Article in journal (Refereed)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from the Shiga-toxin producing Escherichia coli O63 has been elucidated using a combination of bioinformatics, component analyses and NMR spectroscopy. The O-antigen is comprised of tetrasaccharide repeating units with the following structure: 2)--d-Quip3N(d-allo-ThrAc)-(12)--d-Ribf-(14)--d-Galp-(13)--d-GlcpNAc-(1 in which the N-acetylated d-allo-threonine is amide-linked to position 3 of the 3-amino-3-deoxy-d-Quip sugar residue. The presence of a predicted flippase and polymerase encoded in the O63 gene cluster is consistent with the Wzx/Wzy biosynthetic pathway and consequently the biological repeating unit has likely an N-acetyl-d-glucosamine residue at its reducing end. A bioinformatics approach based on predictive glycosyltransferase function present in ECODAB (E. coli O-antigen database) suggested the structural element -d-Galp-(13)-d-GlcpNAc in the O-antigen. Notably, multiple gene sequence alignment of fdtA and qdtA from E. coli to that in E. coli O63 resulted in discrimination between the two, confirmation of the latter in E. coli O63, and consequently, together with qdtB, biosynthesis of dTDP-d-Quip3N. The E. coli O63 O-antigen polysaccharide differs in two aspects from that of E. coli O114 where the latter carries instead an l-serine residue, and the glycosidic linkage positions to and from the Quip3N residue are both changed. The structural characterization of the O63 antigen repeat supports the predicted functional assignment of the O-antigen cluster genes.

  • 9. von der Lieth, Claus-Wilhelm
    et al.
    Ardà Freire, Ana
    Blank, Dennis
    Campbell, Matthew P.
    Ceroni, Alessio
    Damerell, David R.
    Dell, Anne
    Dwek, Raymond A.
    Ernst, Beat
    Fogh, Rasmus
    Frank, Martin
    Geyer, Hildegard
    Geyer, Rudolf
    Harrison, Mathew J.
    Henrick, Kim
    Herget, Stefan
    Hull, William E.
    Ionides, John
    Joshi, Hiren J.
    Kamerling, Johannis P.
    Leeflang, Bas R.
    Lütteke, Thomas
    Lundborg, Magnus
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Maass, Kai
    Merry, Anthony
    Ranzinger, René
    Rosen, Jimmy
    Royle, Louise
    Rudd, Pauline M.
    Schloissnig, Siegfried
    Stenutz, Roland
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Vranken, Wim F.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Haslam, Stuart M.
    EUROCarbDB: an open-access platform for glycoinformatics2011In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 21, no 4, p. 493-502Article in journal (Refereed)
    Abstract [en]

    The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.

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