Detection and impact of genome rearrangement in Salmonella

Tucker, Liam (2021) Detection and impact of genome rearrangement in Salmonella. Masters thesis, University of East Anglia.

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Abstract

The species Salmonella enterica subspecies enterica is responsible for both localised gastrointestinal infections (commonly referred to as food poisoning) and severe systemic infections. Salmonella Typhi is the causative agent of Typhoid fever with an estimated 22 million cases annually, maintaining a presence in select regions of the world despite vaccination programs, with certain regions being more endemic due to either remoteness or political issues. Asymptomatic carriers are critical to the proliferation of Typhi through constant bacterial shedding into the environment. S. enterica can rearrange its genome around the seven ribosomal operons found across the genome via homologous recombination, a phenomenon originally discovered in Typhi carriage isolates. This work’s hypothesis is that the ability to rearrange affects gene expression via gene dosage and growth rate via ori-ter balancing. In this work I establish a method to 1) induce genome rearrangement in bacterial samples within the laboratory, 2) extract high quality DNA and sequence these extracts and 3) analyse the sequence data to determine their genome arrangement. Following this method, I generated a rearrangement (LAT2, a strain derived from BRD948) through long term culturing that I characterised further using growth curve analysis and transcriptomics via RNA sequencing. I analysed the RNA data for differential gene expression which revealed many genes upregulated and downregulated in the LAT2 arrangement, in accordance with their shift in genomic position, relative to oriC. Key genes affected in this rearrangement were genes in the rfb and cyo clusters as well as ackA and pta, with these genes having a role in surface adhesion, survival under stress, and global signalling respectively. My work shows that sequencing provides a scalable alternative to PCR-based determination of genome rearrangement, and that rearrangement impacts upon both growth rate and specifically expression of genes that have changed location relative to the origin of replication.

Item Type:	Thesis (Masters)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	22 Mar 2022 09:39
Last Modified:	22 Mar 2022 09:39
URI:	https://ueaeprints.uea.ac.uk/id/eprint/84205
DOI:

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