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Structure Elucidations of Bacterial Polysaccharides using NMR Spectroscopy and Bioinformatics
Stockholm University, Faculty of Science, Department of Organic Chemistry. (Widmalm)ORCID iD: 0000-0001-5657-8635
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Carbohydrates are ubiquitous components in nature involved in a range of tasks. They cover every cell and contribute both structural stability as well as identity. Lipopolysaccharides are the outermost exposed part of the bacterial cell wall and the primary target for host-pathogen recognition. Understanding the structure and biosynthesis of these polysaccharides is crucial to combat disease and develop new medicine. Structural determinations can be carried out using NMR spectroscopy, a powerful tool giving information on an atomistic scale. This thesis is focused on method development to study polysaccharide structures as well as application on bacterial lipopolysaccharides. The focus has been to incorporate a bioinformatics approach prior to analysis by NMR spectroscopy, and then computer assisted methods to aid in the subsequent analysis of the spectra.

The third chapter deals with the recent developments of ECODAB, a tool that can help predict structural fragments in Escherichia coli O-antigens. It was migrated to a relational database and the aforementioned predictions can now be made automatically by ECODAB. The fourth chapter gives insight into the program CASPER, a computer program that helps with structure determination of oligo- and polysaccharides. An approach to determine substituent positions in polysaccharides was investigated. The underlying database was also expanded and the improved capabilities were demonstrated by determining O-antigenic structures that could not previously be solved. The fifth chapter is an application to O‑antigen structures of E. coli strains. This is done by a combination of NMR spectroscopy and bioinformatics to predict components as well as linkages prior to spectra analysis. In the first case, a full structure elucidation was performed on E. coli serogroup O63, and in the second case a demonstration of the bioinformatics approach is done to E. coli serogroup O93. In the sixth chapter, a new version of the CarbBuilder software is presented. This includes a more robust building algorithm that helps build sterically crowded polysaccharide structures, as well as a general expansion of possible components. 

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University , 2017. , p. 65
Keywords [en]
Carbohydrates, Bioinformatics, NMR Spectroscopy, Lipopolysaccharide, Glycosyltransferase, Computer-Assisted Structure Elucidation, O-antigen, Biosynthesis
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-146867ISBN: 978-91-7649-952-8 (print)ISBN: 978-91-7649-953-5 (electronic)OAI: oai:DiVA.org:su-146867DiVA, id: diva2:1141099
Public defence
2017-10-27, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 5: Manuscript.

Available from: 2017-10-04 Created: 2017-09-13 Last updated: 2017-10-04Bibliographically approved
List of papers
1. Development of the ECODAB into a relational database for Escherichia coli O-antigens and other bacterial polysaccharides
Open this publication in new window or tab >>Development of the ECODAB into a relational database for Escherichia coli O-antigens and other bacterial polysaccharides
2015 (English)In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 25, no 3, p. 341-347Article in journal (Refereed) Published
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.

Keywords
database, ECODAB, Escherichia coli, glycosyltransferase specificity, O-antigen
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-116533 (URN)10.1093/glycob/cwu116 (DOI)000350902900010 ()25352573 (PubMedID)
Funder
Swedish Research Council
Note

AuthorCount:4;

Available from: 2015-05-04 Created: 2015-04-21 Last updated: 2018-03-20Bibliographically approved
2. NMR Chemical Shift Predictions and Structural Elucidation of Oligo- and Polysaccharides by the Computer Program CASPER
Open this publication in new window or tab >>NMR Chemical Shift Predictions and Structural Elucidation of Oligo- and Polysaccharides by the Computer Program CASPER
2017 (English)In: NMR in Glycoscience and Glycotechnology / [ed] Koichi Kato, Thomas Peters, Royal Society of Chemistry, 2017, p. 335-352Chapter in book (Refereed)
Abstract [en]

Glycans are often linked to proteins or lipids in the form of glycoconjugates but these highly complex molecules also have biological functions as oligosaccharides per se. The limited dispersion in NMR spectra of carbohydrates makes their analysis and interpretation very cumbersome. The computer program CASPER, which is a web-based tool, facilitates prediction 1H and 13C NMR chemical shifts of oligo- or polysaccharide structures defined by the user, makes it possible to carry out an NMR-based sugar analysis including determination of absolute configuration and to perform structure elucidation of unknown glycans using unassigned NMR spectra as input to the program. The output from the program contains, inter alia, tentatively assigned NMR resonances, proposed sugar components, structural suggestions ranked according to the similarity between their predicted chemical shifts and the experimental data as well as 3D structures in pdb-format generated seamlessly by the CarbBuilder program as a part of the CASPER-GUI.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2017
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-146862 (URN)978-1-78262-310-6 (ISBN)978-1-78801-128-0 (ISBN)
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2017-09-14Bibliographically approved
3. Structural studies of the O-antigen polysaccharide from Escherichia coli O63 and biosynthetic aspects thereof
Open this publication in new window or tab >>Structural studies of the O-antigen polysaccharide from Escherichia coli O63 and biosynthetic aspects thereof
(English)Manuscript (preprint) (Other academic)
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-146865 (URN)
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2017-09-14Bibliographically approved
4. CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures
Open this publication in new window or tab >>CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures
2016 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 22, p. 2098-2105Article in journal (Refereed) Published
Abstract [en]

CarbBuilder is a portable software tool for producing three-dimensional molecular models of carbohydrates from the simple text specification of a primary structure. CarbBuilder can generate a wide variety of carbohydrate structures, ranging from monosaccharides to large, branched polysaccharides. Version 2.0 of the software, described in this article, supports monosaccharides of both mammalian and bacterial origin and a range of substituents for derivatization of individual sugar residues. This improved version has a sophisticated building algorithm to explore the range of possible conformations for a specified carbohydrate molecule. Illustrative examples of models of complex polysaccharides produced by CarbBuilder demonstrate the capabilities of the software. CarbBuilder is freely available under the Artistic License 2.0.

Keywords
carbohydrate, polysaccharide conformation, C, Albicans, 3D model, Shigella flexneri
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-133371 (URN)10.1002/jcc.24428 (DOI)000379941300007 ()27317625 (PubMedID)
Funder
Swedish Research Council
Available from: 2016-09-12 Created: 2016-09-06 Last updated: 2018-10-18Bibliographically approved
5. Complete 1H and 13C NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER
Open this publication in new window or tab >>Complete 1H and 13C NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-146864 (URN)
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2018-03-27Bibliographically approved

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