Stiens, Jennifer Jane (2025) Using global genomic and transcriptomic approaches to explore host specificity and the role of non-coding RNA in the Mycobacterium tuberculosis complex. PhD thesis, Birkbeck, University of London.
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Stiens J, final thesis for library.pdf - Full Version Download (19MB) |
Abstract
Human-adapted Mycobacterium tuberculosis and animal-adapted Mycobacterium bovis are members of the Mycobacterium tuberculosis complex (MTBC) with nearly identical genomes but different host preferences. In this thesis, the basis for these phenotypic differences is explored using global assays. Transposon insertion sequencing (tn-seq) is used to identify the essential genes for both species in in vitro growth in identical conditions. Differences in the importance of genes involved in nitrogen and sulfur assimilation, and lipid and amino acid metabolism, highlight the evolution of metabolic adjustments made to exploit a microecological niche in a particular mammalian host. M. tuberculosis and M. bovis are reported to be differently sensitive to oxidative stress and tn-seq was also used to determine conditional gene requirements for M. bovis under oxidative stress with menadione treatment. A fatty-acid ligase, fadD30 and an iron transport regulator, irtA, were only conditionally essential with oxidative stress in M. bovis but essential for in vitro growth in M. tuberculosis. Regulation of these differently-required genes may be influenced by the expression of regions outside of protein-coding genes. Transcriptomic studies in both genomes have revealed pervasive non-coding transcription, increasing in stress conditions. Beginning with the best studied member of the MTBC, this thesis begins to address this question by presenting a whole genome co-expression network analysis of M. tuberculosis RNA-seq data to infer the function of these transcripts. This valuable resource can be used by mycobacterial researchers to find potential regulators among predicted non-coding transcripts expressed in a multitude of experimental conditions. Finally, one of these candidate transcripts is investigated using CRISPR inhibition to silence its expression. Antisense-phoR is located within an important regulatory operon, phoPR, which functions at the host-pathogen interface of the MTBC. Antisense silencing impacted sense transcript abundance; perhaps an indication that the transcript plays a role in stabilising phoR mRNA.
Metadata
| Item Type: | Thesis |
|---|---|
| Copyright Holders: | The copyright of this thesis rests with the author, who asserts his/her right to be known as such according to the Copyright Designs and Patents Act 1988. No dealing with the thesis contrary to the copyright or moral rights of the author is permitted. |
| Depositing User: | Acquisitions And Metadata |
| Date Deposited: | 18 Feb 2025 10:56 |
| Last Modified: | 23 Sep 2025 10:19 |
| URI: | https://eprints.bbk.ac.uk/id/eprint/55008 |
| DOI: | https://doi.org/10.18743/PUB.00055008 |
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