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Characterisation of Genomic Islands in Neisseria Meningitidis

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Characterisation of Genomic Islands in Neisseria Meningitidis Characterisation of genomic islands in Neisseria meningitidis Maria Chiara Erminia Catenazzi A Thesis Submitted for the Degree of Doctor of Philosophy (PhD) University of York Department of Biology August 2013 Abstract Neisseria meningitidis asymptomatically colonises the nasopharynx of about 10 % of the human population. This bacterium is an accidental pathogen, with N. meningitidis serogroup B being the main cause of meningitis and septicaemia in developed countries. Strain MC58 has a genome size of 2,272,360 bp and contains 2160 ORFs, more than half of which have already been assigned a function. Nine conserved genomic islands that are absent from the closely related commensal species N. lactamica were identified and comprise 38 genes. Of these, 14 still encode proteins of unknown function. Two of these islands (pathogenic islands 4 and 8) were investigated, and the genes crucial for two further islands (pathogenic islands 3 and 5) involved in polyamine biosynthesis were successfully knocked out in this work. Genomic island 4 contains six genes, which encode proteins that are involved in the 2-methylcitrate pathway; these genes are clustered together to form the prp operon. Several genes belonging to this pathway ( prpC , NMB0432 and ackA-1) were knocked out, and the resulting mutants were unable to utilise propionic acid, which is the substrate for the pathway being investigated. Saliva from over 300 healthy students was analysed for propionic acid content, and the data were compared to the meningococcal carriage status. No significant correlation, however, was found between the concentration of this fatty acid and the carriage status. Genomic island 8 contains coding sequences for the two hypothetical proteins NMB1048 and NMB1049. NMB1049 has been shown to regulate the expression of the divergently transcribed NMB1048 but not prpC . NMB1049 is, in fact, a putative LysR-Type transcriptional regulator. Both genomic islands were also investigated for their involvement in N. meningitidis carriage or infection. Human blood samples from several healthy individuals were inoculated with N. meningitidis MC58, and results showed that only half of the blood samples had bactericidal effects. These results were independent of the strain used, as they were similar for the wild-type and the mutants in the prpC and NMB1049 genes. The catabolism of propionic acid seems to give an advantage to N. meningitidis in colonising the adult nasopharynx. i Table of Contents Abstract ................................................................................................................. i Table of Contents ....................................................................................................... ii List of Figures ........................................................................................................... vii List of Tables ........................................................................................................... xiii List of Abbreviations ............................................................................................... xv Acknowledgements ................................................................................................. xvii Author’s declaration ............................................................................................. xviii Chapter 1 - General introduction ............................................................................ 1 1.1 Microflora present in the oral cavity .............................................................. 1 1.2 Bacteria and the role of propionic acid .......................................................... 3 1.2.1 Propionic acid abundance ....................................................................... 3 1.2.2 Bacteria that synthesise propionic acid .................................................... 4 1.2.3 Pathways generating propionyl-CoA and propionic acid ....................... 5 1.3 Overview of the genus Neisseria ................................................................... 7 1.3.1 Neisseria lactamica ................................................................................. 9 1.3.2 Neisseria gonorrhoeae .......................................................................... 11 1.3.3 Neisseria meningitidis ........................................................................... 11 1.4 Microbiology of Neisseria meningitidis ...................................................... 13 1.5 Carriage and pathogenicity of Neisseria meningitidis ................................. 14 1.6 Vaccine candidates for Neisseria meningitidis ............................................ 17 1.7 Genomic differences between N. meningitidis and the other bacteria ......... 20 1.7.1 Genomic differences between N. meningitidis and . coli ................... 20 1.7.2 Genomic differences between N. lactamica , N. gonorrhoeae and N. meningitidis ........................................................................................... 22 1.8 Aims and objectives of this work ................................................................. 33 ii Chapter 2 - Materials and Methods ....................................................................... 34 2.1 Bacterial strains and plasmids used in this work ......................................... 34 2.1.1 Bacterial strains used in this work ........................................................ 34 2.1.2 Plasmids used in this work .................................................................... 35 2.2 Growth of bacterial strains ........................................................................... 36 2.2.1 Preparation of scherichia coli DH5α and BL21 (DE3) competent cells .............................................................................................................. 36 2.2.2 Growth of scherichia coli DH5α ........................................................ 38 2.2.3 Growth of scherichia coli BL21 (DE3) for overexpression of the protein NMV_1164 ............................................................................... 39 2.2.4 Growth of Neisseria meningitidis ......................................................... 43 2.2.5 Growth of Veillonella spp. for co-culture with Neisseria meningitidis 48 2.2.6 x vivo growth of Neisseria meningitidis in human whole blood ........ 48 2.2.7 Bacterial growth curves ........................................................................ 50 2.2.8 Preparation of . coli cell stocks .......................................................... 50 2.2.9 Preparation of wild-type and mutant N. meningitidis cell stocks ......... 51 2.2.10 Preparation of antibiotic selective media .............................................. 51 2.3 Molecular techniques ................................................................................... 52 2.3.1 Polymerase chain reaction (PCR) ......................................................... 52 2.3.2 pCR® -Blunt II- TOPO® cloning and transformation ......................... 55 2.3.3 Transformation of . coli strain DH5α ................................................. 56 2.3.4 Isolation of plasmid DNA ..................................................................... 56 2.3.5 Preparation of pHP45 $, tetracycline and chloramphenicol cassettes .. 57 2.3.6 Endonuclease restriction digestion of DNA ......................................... 58 2.3.7 Agarose gel electrophoresis and DNA gel extraction ........................... 59 2.3.8 Ligation of DNA fragments .................................................................. 60 2.3.9 TSB transformation of N. meningitidis strain MC58 ............................ 62 2.3.10 Determination of DNA or RNA concentration ..................................... 63 2.3.11 DNA sequencing and data analysis ...................................................... 64 2.3.12 Preparation and purification of total RNA from N. meningitidis ......... 64 2.3.13 Preparation of cDNA ............................................................................ 66 2.3.14 Quantitative Real-Time PCR (RT-PCR) and analysis of gene expression ............................................................................................. 67 iii 2.3.15 Collection and handling of human saliva ............................................. 69 2.4 Analytic chemistry techniques ..................................................................... 70 2.4.1 Gas chromatography (GC) .................................................................... 70 2.5 Protein techniques ........................................................................................ 71 2.5.1 Disruption of cells and preparation of soluble extract .......................... 71 2.5.2 Protein purification ............................................................................... 72 2.5.3 SDS-PAGE ........................................................................................... 73 2.5.4 Coomassie Staining of SDS gels .......................................................... 75 2.5.5 PD-10 Buffer exchange ........................................................................ 75 2.5.6 Quantification with Bradford Assay and storage of proteins ............... 76 2.5.7 Electrophoretic Mobility Shift Assay (EMSA) with DNA 130-mers ... 77 2.5.8 Sybr® Safe and Silver Staining of EMSA gels .................................... 80 2.5.9 Fluorescence Anisotropy ...................................................................... 81 Chapter 3 - Defence against propionic
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