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Title: Patterns of horizontal gene transfer into the Geobacillus clade
Author: Esin, Alexander
ISNI:       0000 0004 7658 7450
Awarding Body: Imperial College London
Current Institution: Imperial College London
Date of Award: 2019
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Horizontal gene transfer (HGT) is the major driver behind rapid bacterial adaptation to a host of diverse environments and conditions. Successful HGT is dependent on overcoming a number of barriers on transfer to a new host, one of which is adhering to the adaptive architecture of the recipient genome. My aim was to investigate how HGT gain is spatially patterned, both on arrival and in long term maintenance. I chose to focus on HGT into a model group of Bacillaceae, that includes Geobacillus spp., not only to avoid ambiguity associated with aggregate analyses, but also because observed biases could enhance our ability to engineer this emerging chassis. In this thesis I first present my methodology for detecting HGT into a specific group; I augmented existing approaches to improve computational tractability while deriving a stringent set of horizontally transferred (HT) gene predictions. In the second results chapter, I assess the predicted HGTs in the context of previous work to find that they are highly consistent, justifying my detection approach. Finally, I dissect the topology of HT genes across Geobacillus genomes to find three large zones of contiguous HGT enrichment. I find that this patterning is driven by gene function, with metabolic genes clustering towards the terminus. Interestingly, the HGT-rich origin-proximal zones, home to many HT genes involved in membrane biogenesis, overlap with the section of the chromosome trapped within the nascent endospore during sporulation. Similar functional enrichment patterns are found in other spore-forming Bacilli, but not those unable to sporulate. This suggests that HGT flow into Geobacillus genomes may be spatially constrained, at least in part, by the sporulation program. In the final chapter, I discuss the implications of this research in a bioengineering context, and suggest possible future directions to confirm the link between HGT topology and sporulation.
Supervisor: Warnecke, Tobias ; Ellis, Tom Sponsor: Imperial College London ; Medical Research Council
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral