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Plasmid genomic studies of the large phytosphere associated plasmid pQBR103

Tett, Adrian James. 2007. Plasmid genomic studies of the large phytosphere associated plasmid pQBR103. PhD Thesis, Cardiff University.

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pQBR103 is a representative of the large pQBR collection of ecologically well characterised self-transmissible and mercury resistant plasmids. These plasmids constitute five genetically distinct groups (I-V) and were isolated from the phytosphere of a number of plant species at a single geographical location. Of the collection pQBR103 (group I), which is known to confer a seasonal fitness benefit on a pseudomonad host, is the best studied. Determination and annotation of the pQBR103 sequence, in this thesis, has revealed it is large at 425 kb, and contains no 16S rRNA or other host "housekeeping" genes. It also revealed the likely mechanisms of plasmid replication and stability, but not of plasmid transfer. While traits of possible ecological function were identified, 80% of coding sequences could not be ascribed a function and 59% of the total coding capacity of pQBR103 constituted novel orphan genes. Therefore, the ecological function of this plasmid remains largely enigmatic. Having created an online database, of all publicly available complete plasmid genomes, the lack of functional assignment to pQBR103 may reflect the biases in plasmids previously chosen for sequencing. Building on the legacy of the plasmid sequence, genomic investigations were undertaken. In vitro, proteomic studies demonstrated pQBR103 is tightly regulated and affects host chromosomal responses to the environment. Diversity within the pQBR collection (groups I, III and IV) was assessed by PCR surveys and a custom pQBR103 microarray. Intergroup comparisons revealed no shared homology between group I and groups III or IV, other than common mer genes, suggesting independent evolutionary histories. Intragroup comparisons identified genetic instability and revealed a common genetic core, which contains the genes putatively responsible for stability and replication. These features are not clustered and there are relatively few repeat sequences, both of which contradict the modular paradigm described for other plasmids.

Item Type: Thesis (PhD)
Status: Unpublished
Schools: Biosciences
Subjects: Q Science > QR Microbiology
ISBN: 9781303181863
Date of First Compliant Deposit: 30 March 2016
Last Modified: 12 Feb 2016 23:14

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