Investigation into plasmid replication and partitioning systems in proteobacteria

Thanks to the development of numerous sequencing projects, a large volume of publicly available bacterial genomic information has accumulated. Relatively little, however, has been published regarding plasmid backbone systems based on public genomes. More specifically, a comprehensive analysis of plasmid replication and partitioning systems that would investigate their distribution and evolutionary history across bacteria is lacking. This thesis firstly developed a database for the plasmid backbone systems in proteobacteria. Using the database as a platform, eight major families of plasmid replication systems and five major families of plasmid partitioning systems, both of which are abundant in proteobacteria, were identified and a phylogenetic analysis for each family was performed. For the replication systems in proteobacteria, it was found that most plasmids do not show a wide host range, especially over class or phylum level, except for those that are already well known as broad host range plasmids, which, nevertheless, have a variety of replication systems. Plasmids, however, have been shown to move at least between related hosts, particularly within an order or class level. Regarding partitioning systems, four discrete ParA types of Type I class in partitioning modules were characterized according to their partner protein ParB. Based on the phylogenetic results, partitioning systems are also restricted to the class level. The members of each type do not seem to move outside the class level, except in the case of broad host range plasmids. This thesis has suggested that Rep initiators can be a good marker for classification. In particular, their phylogeny might be a reliable indicator of incompatibility between plasmids. Partitioning modules are a factor in the analysis, but it has been verified that in some cases the Rep and Par cannot identify the incompatibility groups. Through the case study of Rep and Par systems in 72 Rhizobium leguminosarum strains, this thesis demonstrated that although there is no movement of large plasmids between species, there are some cases indicating the possible horizontal transfer for relatively small plasmids between species. Finally, it was observed that there are cases of movement between strains, which might act as a vehicle for specific accessory genes, or might reflect a variety of intracellular recombination.