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Structure Elucidations of Bacterial Polysaccharides Using Nmr Spectroscopy and Bioinformatics

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Structure Elucidations of Bacterial Polysaccharides Using Nmr Spectroscopy and Bioinformatics ! "#! #"$"" %& '( ) ' *#+,$ - $. / $0 1 / $ / $ 2%3 ' / $ . / $ . 2%3 ' - $ . / 4,' $ 5 / / 4,$. 43' / $ / $ . / 1 / $. 6 $. 2%3 / $5 ' / +7' 87$ 5 1 '/ , / $. / ' / 1 $ ! " ! " "#! 9:: $$ : ; < 99 9 9 #=+>+! 5,28!>8#!+=88? > 5,28!>8#!+=88?7? # $ % '#"+8# STRUCTURE ELUCIDATIONS OF BACTERIAL POLYSACCHARIDES USING NMR SPECTROSCOPY AND BIOINFORMATICS Jonas Ståhle Structure Elucidations of Bacterial Polysaccharides using NMR Spectroscopy and Bioinformatics Jonas Ståhle ©Jonas Ståhle, Stockholm University 2017 ISBN print 978-91-7649-952-8 ISBN PDF 978-91-7649-953-5 Cover Picture: kolhydratskurbits Printed by Universitetsservice US-AB, Stockholm 2017 Distributor: Department of Organic Chemistry ӏ್峯峫岾峇 ෫್峯峫岾峇 ઉ峘峯Ո峛ॷ峂್峯峫岾峙 ৐෋峗岸島屺峿峯峎 ཋ峜峗岼 ݀峄峓ᛊ岣峇 岱峑峯峄峇岸್峼島峐峓峽峸 ݣ࣑ୖٸ Abstract 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. v List of Publications This thesis is based on the following papers, which will be referred to by Roman numerals I – V. Reprints were made with the kind permission of the publishers. I. Development of the ECODAB into a Relational Database for Escherichia coli O-antigens and other Bacterial Polysaccharides Thomas Lütteke and Göran ,ۆJonas Ståhle ,ۆMiguel A. Rojas-Macias Widmalm. Glycobiology, 2014, 25(3), 341-347 II. NMR Chemical Shifts Predictions and Structural Elucidation of Oligo- and Polysaccharides by the Computer Program CASPER Jonas Ståhle and Göran Widmalm NMR in Glycoscience and Glycotechnology, 2017, 335-352 III. Structural Studies of the O-antigen Polysaccharide from Escherichia coli O63 and Biosynthetic Aspects Thereof Jonas Ståhle, Carolina Fontana, Andrej Weintraub and Göran Widmalm In manuscript IV. CarbBuilder: Software for Building Molecular Models of Complex Oligo- and Polysaccharide Structures Michelle M. Kuttel, Jonas Ståhle and Göran Widmalm Journal of Computational Chemistry, 2016, 37(22), 2098-2105 V. 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 Thibault Angles d’Ortoli, Hani Mobarak, Jonas Ståhle, Christoffer Hamark, Carolina Fontana, Olof Engström, Patricia Apostolica and Göran Widmalm In manuscript Authors contributed equally to this workۆ vii Related papers and book sections by the author not included in the thesis: Complete 1H and 13C NMR Chemical Shift Assignments of Mono- to Tetrasaccharides as Basis for NMR Chemical Shift Predictions of Oligosaccharides Using the Computer Program CASPER Jerk Rönnols, Robert Pendrill, Carolina Fontana, Christoffer Hamark, Thibault Angles d’Ortoli, Olof Engström, Jonas Ståhle, Mona V. Zaccheus, Elin Säwén, Liljan E. Hahn, Shahzad Iqbal and Göran Widmalm Carbohydrate Research, 2013, 380, 156-166 Serotype-Conversion in Shigella flexneri: Identification of a Novel Bacteriophage, Sf101, from a Serotype 7a Strain Richa Jakhetia, Aruna Marri, Jonas Ståhle, Göran Widmalm and Naresh K. Verma BMC Genomics, 2014, 15:742 Exploration of the Active SLWHRIȕ*DO7Modifications of the Aglycon of Aromatic Xylosides Anna Siegbahn, Karin Thorsheim, Jonas Ståhle, Sophie Manner, Christoffer Hamark, Andrea Persson, Emil Tykesson, Katrin Mani, Gunilla Westergren- Thorsson, Göran Widmalm and Ulf Ellervik Organic and Biomolecular Chemistry, 2015, 13(11), 3351-3362 Structural Studies of Lipopolysaccharide-Defective Mutants from Brucella melitensis Identify a Core Oligosaccharide Critical in Virulence Carolina Fontana, Raquel Conde-Álvarez, Jonas Ståhle, Otto Holst, Maite Iriarte, Yun Zhao, Vilma Arce-Gorvel, Seán Hanniffy, Jean-Pierre Gorvel, Ignacio Moriyón and Göran Widmalm The Journal of Biological Chemistry, 2016, 291(14), 7727-7741 Databases and $VVRFLDWHG7RROVIRU*O\FRSURWHRPLFV Frederique Lisacek, Julien Mariethoz, Davide Alocci, Pauline M. Rudd, Jodie L. Abrahams, Matthew P. Campbell, Nicolle H. Packer, Jonas Ståhle, Göran Widmalm, Elaine Mullen, Barbara Adamczyk, Miguel A. Rojas- Macias, Chunsheng Jin and Niclas G. Karlsson Methods in Molecular Biology, 2017, 1503:235-264 Structural Characterization of an all-Aminosugar-Containing Capsular Polysaccharide from Colwellia psychrerythraea 34H Angela Casillo, Jonas Ståhle, Ermenegilda Parrilli, Filomena Sannino, Daniel E. Mitchell, Giuseppina Pieretti, Matthew I. Gibson, Gennaro Marino, Rosa Lanzetta, Michelangelo Parrilli, Göran Widmalm, Maria L. Tutino and Maria M. Corsaro Antonie van Leeuwenhoek, 2017, Epub ahead of print, doi: 10.1007/s10482- 017-0834-6 viii Abbreviations ABC-transporter ATP-binding cassette-transporter Abe Abequose BLAST Basic Local Assignment Search Tool BRU Biological repeating unit CASE Computer-aided structure elucidation CASPER Computer Assisted SPectrum Evaluation of Regular polysaccharides CMP Cytidine 5'-Monophosphate COSY Correlation spectroscopy dTDP Thymidine 5'-diphosphate ECA Enterobacterial common antigen ECODAB E. coli O-antigen database EPS Exo-polysaccharide FID Free induction decay g Gauche Fuc Fucose Gal Galactose GalNAc N-acetyl galactosamine GC Gas chromatography GDP Guanosine 5'-diphosphate Glc Glucose GlcA Glucuronic acid GlcNAc N-acetyl glucosamine GT Glycosyltransferase H2BC Heteronuclear two-bond correlation HETCOR Heteronuclear correlation HMBC Heteronuclear multiple bond correlation HSQC Heteronuclear single quantum correlation IM Inner membrane LPS Lipopolysaccharide LPS-OH O-deacetylated lipopolysaccharide Man Mannose NDP Nucleotide diphosphate NMR Nuclear magnetic resonance NOESY Nuclear overhauser effect spectroscopy ix NUS Non-uniform sampling OM Outer membrane PEG Polyethylene glycol PHPT Polyisoprenyl-phosphate hexose-1-phosphate transferases PNPT Polyisoprenyl-phosphate N-acetylaminosugar-1- phosphate transferases PS Polysaccharide Qui3NAc 3-N-acetyl quinovosamine Ribf Ribofuranose RRMSD Regional root-mean-square deviation SNFG Symbol nomenclature for glycans STEC Shiga toxin producing E. coli t Trans TFA Trifluoro acetic acid TOCSY Total correlation spectroscopy UDP Uridine 5'-diphosphate Und-PP Undecaprenyl-diphosphate x Contents Abstract ....................................................................................................................... v List of Publications .................................................................................................. vii Abbreviations ............................................................................................................. ix 1 Introduction ...................................................................................................... 1 1.1 Biological relevance of carbohydrates ......................................................... 1 1.2 Carbohydrate structure................................................................................. 1 1.2.1 Basics ................................................................................................ 1 1.2.2 Carbohydrate conformation
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