Transcription Factor Network Regulates E. coli’s Genome-wide Stress-response

Bilena Lima de Brito Almeida

Research output: Book/ReportDoctoral thesisCollection of Articles


Recent developments in Molecular Biology and Bioinformatics have allowed us to dissect the Gene Regulatory Network (GRN) of the model organism Escherichia coli (E. coli). However, even for this organism, it remains challenging to find relationships between the structure and dynamics of its GRN. In general, it is well established that the responses of bacteria, such as E. coli, to major stresses that occur in the oral-fecal route (e.g., temperature shifts) involve hundreds of genes. However, the properties that render certain genes responsive to those stresses, while leaving other genes unresponsive, have not been discovered yet. Furthermore, the responses to these stresses are usually temporally ordered. First, there is a short-term response that involves a few hundred genes. These responses are usually transient. After a couple of hours, another large cohort of genes changes its activity, which could lead to significant changes in the cellular phenotype.

The mechanisms responsible for these vital, temporally ordered responses to genome-wide stresses have been investigated in this thesis. To achieve this, similar to a few recent studies, E. coli cells were subjected to perturbations affecting many genes. Subsequently, the genes' response at the RNA (ribonucleic acid) level was measured. In addition, detailed information on each and every interaction made possible by Transcription Factors (TFs) of the E. coli’s GRN, as well as other properties such as the genes' sequence, among others, was collected using databases. With this information, quantitative relationships between the structure and dynamics of the E. coli’s GRN (including the TF Network, TFN) were searched for. Overall, the studies conducted contribute to a better understanding of how the global properties of the GRN of E. coli contribute to the genome-wide transcriptional programs that are responsive to the most important stresses that these cells endure throughout their lifetime in natural environments.

In detail, first, a short study was conducted on the effects of shifts in RNA Polymerase (RNAP) concentrations in individual bacterial cells. It was observed that the mean and cell-to-cell variability in RNAP levels exhibit a correlation with the cellular morphology and composition. This correlation implies that alterations in RNAP levels result in quick effects on the GRN of E. coli, subsequently influencing cell morphology and physiology.

Based on those results, it was then hypothesized that quick changes in RNAP concentrations due to medium shifts would lead to quick, genome-wide changes in the RNA numbers of E. coli cells. Furthermore, these changes would probably be further propagated by TFs to the nearest neighbors in the TFN. Potentially, these changes in individual genes could be quasi-synchronous and, in that case, the global propagation of signals throughout the E. coli’s GRN could be investigated based on this perturbation alone. Interestingly, a close relationship between the response dynamics of genes directly linked by TFs was found in the study conducted in this thesis. More importantly, on average, at the genome-wide level, the mid-term responses of the genes were determined by a cumulative effect of the changes in the abundances of the input TFs of each gene.

Next, a similar study was performed by stressing cells with cold shocks instead. The genes' response to cold shock was compared with their response to an antibiotic, Novobiocin (known to block DNA (deoxyribonucleic acid) gyrase, which resolves Positive Supercoiling Buildups, PSBs, via an endothermic process). It was found that nearly half of the genes responsive to cold shock are also responsive to Novobiocin. This, along with additional measurements, allowed the establishment that many genes are responsive to cold shock because they are sensitive to PSB.
Original languageEnglish
Place of PublicationTampere
ISBN (Electronic)978-952-03-3202-0
Publication statusPublished - 2024
Publication typeG5 Doctoral dissertation (articles)

Publication series

NameTampere University Dissertations - Tampereen yliopiston väitöskirjat
ISSN (Print)2489-9860
ISSN (Electronic)2490-0028


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