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Structural and Functional Studies of the Heptose Modifying Enzymes That Play a Role in Campylobacter Jejuni Virulence

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Structural and Functional Studies of the Heptose Modifying Enzymes That Play a Role in Campylobacter Jejuni Virulence Western University Scholarship@Western Electronic Thesis and Dissertation Repository 1-15-2016 12:00 AM Structural and functional studies of the heptose modifying enzymes that play a role in Campylobacter jejuni virulence. Heba Soliman Barnawi The University of Western Ontario Supervisor Dr. Carole Creuzenet The University of Western Ontario Graduate Program in Microbiology and Immunology A thesis submitted in partial fulfillment of the equirr ements for the degree in Master of Science © Heba Soliman Barnawi 2016 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Microbiology Commons, Molecular Biology Commons, and the Structural Biology Commons Recommended Citation Barnawi, Heba Soliman, "Structural and functional studies of the heptose modifying enzymes that play a role in Campylobacter jejuni virulence." (2016). Electronic Thesis and Dissertation Repository. 3478. https://ir.lib.uwo.ca/etd/3478 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. ABSTRACT Campylobacter jejuni is a major cause of gastroenteritis in humans. The capsule of some species contains unique modified heptoses. Heptose modification and novel epimerases and reductases were identified for C. jejuni NCTC11168 and 18-176. We hypothesized that heptose modifying enzymes in C. jejuni have specific catalytic residues that allow for substrate and product specificity. Substrate synthesis, structural modeling, point mutations, and enzymatic analysis have been applied to map the active sites. Putative catalytic residues showed substrate and/or product specificity. The epimerases structures were solved by crystallography done by our collaborator. We also hypothesized that synthesis of the modified heptoses is important for biofilm formation. In vitro experiment of C. jejuni NCTC11168 showed that the heptose modefication biosynthesis mutants have a significant reduction in biofilm formation under aerobic conditions. This project has provided essential information about the structure and mechanism of heptose modifying enzymes. It also will emphasize their importance in some C. jejuni virulence properties such as biofilm formation. Keywords: Campylobacter jejuni, Modified heptose, Epimerase, Reductase, Structure, binding site, Biofilm. CO-AUTHORSHIP The crystallography structures’ PDB files for the epimerases were generated by Laura Woodward in Dr. James Naismith laboratory (St. Andrews University, UK) and the structure view was modified using PyMol software to generate the figures represented in this thesis by us. The site-directed mutagenesis of the epimerases mutants (DdahB- N121S, MlghB-N121S, H67A, Y134F) and the reductases mutants were generated by Michael Roubakha. MlghB-Y132F mutant was created, expressed and purified by Chelsea Kubinec. She was also involved in confirming the enzymatic activity of MlghB mutants using different enzymes stocks. The GDP-manno-heptose substrate that was used in all enzymatic activity was kindly provided by Dr. Creuzenet. The mutant strains that were used in the biofilm assay were previously generated by Anthony Wong and Dirk Lange. The work conducted by me in this project was expressing and purifying all the wild type and the mutants’ enzymes. In addition, I also performed all enzymatic analyses, kinetics, homology modeling, and the first two steps of GDP-manno-heptose synthesis. ii ACKNOWLEDGMENT I would like to express my deepest gratitude to my supervisor, Dr. Carole Creuzenet for giving me this great opportunity to conduct this research in her lab. Special thanks for her continued guidance, support, motivation, and patience. I would also like to thank my advisory committee members, Dr. John McCormick and Dr. Gary Shaw for their helpful advice and suggestions. I also extend my thanks to the department office staff, Fernanda Russell, Kim Arts, and Fred Williams for their help with administrative matters. I would like to thank all members of the Dr. Creuzenet lab, past and present for every help they provided to me during my studies. Special thanks to Najwa Zebian for her invaluable assistance and her continued support and kindness. Thanks to her for being such a great motivating friend and of kind assistance. I am also grateful to the Ministry of Higher Education of Saudi Arabia, the University of Hail, and the Saudi Cultural Bureau for their financial and academic support. Without this support, I would not be able to have this great chance to pursue this MSc studies. Finally, I would like to extend my sincere gratitude to the ones who strongly supported me from the beginning to the very last moment of this journey, my family. Thanks to my father Soliman and my mother Salma for the endless prayers and support. Thanks for enduring all the difficulties of sending me abroad to achieve my goals. To my siblings Rashad, Elham, and the rest of my family for keeping me motivated. iii TABLE OF CONTENTS ABSTRACT .................................................................................................................... i CO-AUTHORSHIP ........................................................................................................ ii ACKNOWLEDGMENT ............................................................................................... iii TABLE OF CONTENTS ............................................................................................... iv LIST OF FIGURES ..................................................................................................... viii LIST OF TABLES ..........................................................................................................x LIST OF ABBREVIATIONS ........................................................................................ xi CHAPTER 1- INTRODUCTION .................................................................................1 1.1. Campylobacter jejuni ............................................................................................2 1.1.1. History and taxonomy ...............................................................................2 1.1.2. General characteristics ..............................................................................2 1.2. Epidemiology and pathogenesis ............................................................................3 1.3. Clinical characteristics ..........................................................................................4 1.3.1. Induced enteritis and immune response .....................................................4 1.3.2. Immunological neuromuscular disorders ...................................................5 1.3.2.1. Guillain-Barre Syndrome (GBS) ......................................................5 1.3.2.2. Miller Fisher syndrome (MFS) .........................................................6 1.4. Virulence factors ...................................................................................................6 1.4.1. Adhesion and invasion ..............................................................................6 1.4.2. Intracellular survival .................................................................................7 1.4.3. Biofilm formation .....................................................................................8 1.4.4. Flagella and motility .................................................................................9 1.4.5. Glycosylation .......................................................................................... 10 1.4.6. Lipooligosaccharide (LOS) ..................................................................... 11 1.4.7. Capsule polysaccharide (CPS)................................................................. 12 1.4.7.1. CPS genetics .................................................................................. 15 1.4.7.2. CPS synthesis ................................................................................ 16 1.4.7.3. Biological role in virulence ............................................................ 21 1.5. GDP-manno-heptose synthesis ............................................................................ 22 1.6. C. jejuni GDP-manno-heptose modification ........................................................ 24 iv 1.6.1. The modified heptose role in virulence .................................................... 24 1.6.2. The modified heptose synthesis enzymes ................................................ 27 1.6.3. The modified heptose synthesis pathways ............................................... 27 1.7. Enzymes structure ............................................................................................... 32 1.7.1. Homology modeling ............................................................................... 32 1.7.2. X-ray crystallography ............................................................................. 33 1.8. Enzymes active site ............................................................................................. 34 1.9. Rational and hypothesis ...................................................................................... 36 1.10. Objectives ....................................................................................................... 37 CHAPTER 2 – MATERIAL AND METHODS ......................................................... 38 2.1. Bacterial
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