Ren, Chuan-Peng
(2010).
Comparative Genomics of Selected Species of Gram-Negative Bacteria.
University of Birmingham.
Ph.D.
Abstract
Investigation of genomic diversity can provide insight into the evolutionary history of bacterial species. However, complete genome sequencing is not yet practical for large strain collections at the beginning of this project. In this project PCR-based methods to investigate the genomic diversity of non-sequenced strains were successfully developed. In \(Escherichia\) \(coli\), the distribution of two Type III secretion system, ETT2 (\(E.\) \(coli\) Type Three Secretion 2) and Flag-2 (\(E.\) \(coli\) Flagellar system 2), were surveyed among a collection of 79 strains. Remnants of both clusters were found to be present in most strains, suggesting that both have a long evolutionary history within \(E.\) \(coli\). The PCR-based methods were also developed for application as part of genome sequencing projects. They were used to explore the co-linear and variable regions between \(Campylobacter\) \(jejuni\) M1 and the genome sequenced strain \(C.\) \(jejuni\) strain 11168. The \(C.\) \(jejuni\) M1 genome was assembled into thirty-four genomic contigs relative to strain 11168, and the size and position of insertions/deletions were characterised. Similar methods were used to facilitate the finishing of the genome of \(Francisella\) \(tularensis\) strain FSC198, using sequence information from strain Schu S4. The completed genome sequence of FSC198 showed it to be almost identical to that of Schu S4. The two genomes differ at only 11 loci, eight SNPs (single nucleotide polymorphisms) and 3 VNTRs (variable number tandem repeats). This surprising finding suggested that the European isolate FSC198 may be derived from the US laboratory strain Schu S4. Two virulence factors, IglA and IglB, from a pathogenicity island of strain FSC198 were further investigated and found to interact at the protein level. These proteins are possibly involved in Type VI secretion, and may represent potential vaccine candidates.
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