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Characterisation and Structural Studies of a Superoxide Dismutase and Ompa-Like Proteins from Borrelia Burgdorferi Sensu Lato

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Characterisation and Structural Studies of a Superoxide Dismutase and Ompa-Like Proteins from Borrelia Burgdorferi Sensu Lato University of Huddersfield Repository Brown, Gemma Characterisation and structural studies of a superoxide dismutase and OmpA-like proteins from Borrelia burgdorferi sensu lato Original Citation Brown, Gemma (2016) Characterisation and structural studies of a superoxide dismutase and OmpA-like proteins from Borrelia burgdorferi sensu lato. Doctoral thesis, University of Huddersfield. This version is available at http://eprints.hud.ac.uk/id/eprint/31870/ The University Repository is a digital collection of the research output of the University, available on Open Access. Copyright and Moral Rights for the items on this site are retained by the individual author and/or other copyright owners. Users may access full items free of charge; copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational or not-for-profit purposes without prior permission or charge, provided: • The authors, title and full bibliographic details is credited in any copy; • A hyperlink and/or URL is included for the original metadata page; and • The content is not changed in any way. For more information, including our policy and submission procedure, please contact the Repository Team at: [email protected]. http://eprints.hud.ac.uk/ Characterisation and structural studies of a superoxide dismutase and OmpA-like proteins from Borrelia burgdorferi sensu lato Gemma Brown BSc A thesis submitted to the University of Huddersfield in partial fulfilment of the requirements for the degree of Doctor of Philosophy July 2016 Page | 1 Copyright declaration i. The author of this thesis (including any appendices and/or schedules to this thesis) owns any copyright in it (the “Copyright”) and he has given The University of Huddersfield the right to use such Copyright for any administrative, promotional, educational and/or teaching purposes. ii. Copies of this thesis, either in full or in extracts, may be made only in accordance with the regulations of the University Library. Details of these regulations may be obtained from the Librarian. This page must form part of any such copies made. iii. The ownership of any patents, designs, trademarks and any and all other intellectual property rights except for the Copyright (the “Intellectual Property Rights”) and any reproductions of copyright works, for example graphs and tables (“Reproductions”), which may be described in this thesis, may not be owned by the author and may be owned by third parties. Such Intellectual Property Rights and Reproductions cannot and must not be made available for use without the prior written permission of the owner(s) of the relevant Intellectual Property Rights and/or Reproductions. Page | 2 For my family Page | 3 “Wine is the most healthful and most hygienic of beverages.” Louis Pasteur, 1822 – 1895. Page | 4 Abstract Lyme borreliosis is the most common tick-borne, human infection across the Northern hemisphere. The agent responsible, Borrelia burgdorferi sensu lato (s.l.) covers a family of Spirochaetes with unique characteristics which are shared by both Gram-negative and Gram- positive bacteria. The outer membrane (OM) is rich in lipoproteins but contains a relatively low density of integral membrane proteins (OMPs), of these OMPs very few have been identified and even fewer are well characterised. The OmpA-like transmembrane domain defined by the Pfam family PF01389 is a 8-stranded membrane spanning β-barrel and is well conserved among Gram-negative bacteria but to date remains unknown in Spirochaetes. Building from previous computational work which had sought to identify possible OMPs from B. burgdorferi s.l. four OmpA-like proteins, BAPKO_0422 (Borrelia afzelii), BB_0562, BB_0406 (B. burgdorferi) and BG0408 (Borrelia garinii) have been identified and structurally characterised. The four proteins are encoded by chromosomal genes and highly conserved between Borrelia species and may be of diagnostic or therapeutic value. Structural characterisation by both circular dichroism and small angle X-ray scattering suggests these four proteins adopt a compact globular structure rich in β-strand (~40%) with Ab initio molecular envelopes resembling a cylindrical peanut shape with dimensions of ~25x45 Å consistent with an 8-stranded β-barrel. The present work demonstrates that BAPKO_0422 can bind human factor H (hfH) and some evidence for a further interaction between the BAPKO_0422 protein and heparin. The interaction with hfH may contribute to the spirochaete’s immune evasion mechanisms by the inhibition of the complement response. The zoonotic life-cycle of Borrelia and challenges by the host’s immune system causes an ever changing environment which often leads to fluctuations of O2 exposure. Although B. burgdorferi s.l. have a distinct lack of metabolic systems including peroxidases and catalase enzymes the Spirochaetes genome does encode a single superoxide dismutase gene (sodA - bb_0157). Previously assigned as a Fe-SOD there has been some debate whether this protein requires iron or manganese as a co-factor. The present work demonstrates that the B. burgdorferi enzyme SodA requires manganese for activity and does not display cambialistic behaviour. Structural and proteomic characterisation suggests the B. burgdorferi SodA enzyme shares significant sequence similarity to a superoxide dismutase from Thermus thermophilus. Page | 5 Table of Contents Copyright declaration 2 Abstract 5 Table of contents 6 List of figures 13 List of tables 18 List of equations 20 Abbreviations 21 Acknowledgements 23 Chapter 1. Introduction 24 1.1. Lyme disease 24 1.1.1. A brief history of Lyme disease 24 1.1.2. Symptoms 25 1.1.3. Diagnosis 31 1.1.4. Treatment and vaccination 33 1.1.5. Post-Lyme disease syndrome (PLDS) 34 1.1.6. Incidence 35 1.1.7. Risk of infection 37 1.2. Ticks 39 1.2.1. Ecology, reservoirs and the tick lifecycle 39 1.2.2. Tick morphology 43 1.2.3. Feeding of ticks and the transmission of Borrelia 43 1.3. Borrelia 45 1.3.1. Spirochaetes and Borrelia 45 1.3.2. The genus Borrelia 45 1.3.3. Relapsing fever Borreliae 46 1.3.4. Genomic complexity 49 1.3.5. Morphology and ultrastructure 51 1.3.6. Alternative morphological states 52 1.4. The Borrelia outer membrane 54 1.4.1. Introduction to the outer membrane and its diagnostic and therapeutic importance 54 1.4.2. Lipoproteins and Borrelia 58 1.4.3. Bacterial integral membrane proteins 59 1.4.3.1. Introduction to beta-barrel proteins 59 Page | 6 1.4.3.2. E. coli – OmpA 63 1.4.3.3. E. coli – OmpX 64 1.4.3.4. E. coli – OmpW 65 1.4.3.5. OmpA-like proteins 66 1.4.3.5.1. Yersinia pestis – Ail 68 1.4.3.5.2. Neisseria – NspA 70 1.4.3.6. OmpA-like proteins and the blood brain barrier 71 1.4.4. Known Borrelia OMPs 75 1.5 Protein expression throughout the enzootic lifecycle 77 1.5.1. Major surface proteins of Borrelia expressed within the tick 77 vector 1.5.2. Borrelia proteins implicated in the early stage of host 80 infection 1.5.3. Borrelia proteins responsible for dissemination and 80 extracellular matrix adhesion 1.5.4 Translocation of Borrelia across the vascular endothelium 83 involvement of the blood brain barrier 1.6. Immune evasion strategies 85 1.6.1 Tick salivary proteins 86 1.6.2 Hijacking plasminogen activation 86 1.6.3 Evading the complement system 88 1.6.4 Surface antigenic variation 93 1.6.5 Oxidative stress and Borrelia superoxide dismutase 96 1.7 Research Aims 99 1.7.1 Borrelia OmpA-like proteins 99 1.7.2 Superoxide dismutase A 102 Chapter 2: Materials and Methods 104 2.1 Materials 104 2.1.1 DNA and Oligonucleotides 104 2.1.2 Reagents, buffers and enzymes 109 2.1.3 Detergents 112 2.1.4 Expression and maintenance E .coli strains 114 2.2 Methods 115 2.2.1 Sequence analysis and BLAST searching 115 2.2.2 Molecular biology 115 Page | 7 2.2.2.1 PCR amplification of gene targets and addition of 115 restriction sites 2.2.2.2 Agarose gels 116 2.2.2.3 DNA quantification 117 2.2.2.4 Restriction digest and ligation of targets and vector 117 2.2.2.5 Competency and transformation 118 2.2.2.6 Restriction analysis and extraction for storage 119 2.2.3 Protein overexpression 119 2.2.3.1 Recombinant protein expression by IPTG 119 2.2.3.2 Recombinant protein expression by auto-induction 120 2.2.3.3 SDS-PAGE and Western blot analysis 120 2.2.3.4 Casting of gels and running conditions 122 2.2.3.5 Western blot analysis 122 2.2.4 Protein extraction and preparation of OMP-A like proteins 124 2.2.4.1 Cell harvesting and lysis 124 2.2.4.2 Inclusion body preparation and solubilisation 124 2.2.5 Protein purification and refolding of OMP-A like proteins 124 2.2.5.1 Immobilised Metal Affinity Chromatography 124 (IMAC) 2.2.5.2 Ion Exchange Chromatography 125 2.2.5.3 Bench top refolding 125 2.2.5.4 On-column refolding 125 2.2.5.5 Removal of the poly-histidine-tag 126 2.2.5.6 Concentration and dialysis of protein samples 126 2.2.5.7 UV absorbance spectrum of refolded protein and 126 quantification 2.2.5.8 Size Exclusion Chromatography (SEC) 127 2.2.6 Characterisation of OMP-A like proteins 129 2.2.6.1 Gel shift assays for Borrelia OMPs 129 2.2.6.2 Phase partitioning of Borrelia OMPs 129 2.2.6.3 Affinity ligand binding assays for Borrelia OMPs 130 2.2.6.4 Immobilised heparin binding assays for Borrelia 131 BAPKO_0422 2.2.7 Protein overexpression and preparation of superoxide 131 dismutase A Page | 8 2.2.7.1 Bacterial Strains, Plasmids, Growth Conditions 131 and Protein Expression 2.2.7.2 Production of apo-protein 132 2.2.7.4 On-column refolding and purification 132 2.2.7.5 Assaying SOD activity 133 2.2.8 Structural Experiments of OMP-A like proteins and SodA 135 2.2.8.1 Circular Dichroism - Sample preparation, data 135 collection and analysis 2.2.8.2 Small Angle X-ray Scattering 136 2.2.8.2.1 Sample preparation and data collection 136 2.2.8.2.2 Data analysis 136 2.2.9 Crystallography of SOD and OMP targets 138 2.2.9.1 Vapour diffusion crystallography 138 2.2.9.2 In meso phase crystallography 139 2.2.10 In silico characterisation and homology modelling 142 of OMPs Chapter 3: Results - Borrelia OMPA-like proteins 145 3.1 Identification of possible OmpA-like proteins in B.
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