Topological Control of Bacterial Stress Adaptation
Jagadeesan, Rahul (2026)
Tampere University
2026
Lääketieteen, biotieteiden ja biolääketieteen tekniikan tohtoriohjelma - Doctoral Programme in Medicine, Biosciences and Biomedical Engineering
Lääketieteen ja terveysteknologian tiedekunta - Faculty of Medicine and Health Technology
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Väitöspäivä
2026-09-03
Julkaisun pysyvä osoite on
https://urn.fi/URN:ISBN:978-952-03-4727-7
https://urn.fi/URN:ISBN:978-952-03-4727-7
Tiivistelmä
Bacteria traverse diverse environments, many of which can be detrimental. To survive these fluctuations, they rely on internal regulatory programs that shape their adaptive responses. These programs are not driven by a universal mechanism, but by the multiple layers of regulatory topologies from global chromosomal structure to local protein flexibility. While many individual mechanisms have been studied in detail, how these topological layers collectively shape genome-wide responses to stress remains poorly understood.
Using Escherichia coli as our model organism, we examined how regulatory topology influences genome-wide adaptation during bacterial stress response. First, we investigated operon topology and how it affects transcriptional responses to stresses involving antibiotics and starvation. By combining transcriptomics, flow cytometry, and synthetic promoter constructs, we show that internal promoters within operons are positioned and tuned in ways that mitigate the transcriptional losses caused by premature transcriptional termination. These losses are further amplified by topological factors such as DNA supercoiling and collisions between elongating and promoter-bound RNA polymerases. Consistent with this, comparative analyses across evolutionarily distant bacteria indicate that similar operon-level transcriptional responses are broadly conserved.
Next, we explored transcription factor network (TFN) dynamics by constructing a library of fluorescent reporters for 16 global regulators, which collectively account ~30% of the E. Coli network topology. These constructs capture promoter-level transcription rates with high sensitivity and specificity under exponential, stationary, weak, and strong stress conditions. The reporters reveal substantial single-cell variability in global regulator (GR) activity and provide a quantitative tool to map the order, timing, and hierarchy of TFN activation during stress.
Finally, we examined how DNA structure, protein conformational flexibility, metabolic and regulatory networks contribute to adaptation under concurrent temperature and antibiotic stresses. We find that during combined exposure, transcriptomes collapse toward temperature-defined states. This dominance arises from topological constraints on nucleoid, ATP-dependent enzymatic activity, induction of global regulatory networks, and the conformational flexibility of antibiotic-target complexes. Cross-species simulations and phylogenetic comparisons suggest that temperature-induced changes in antibiotic efficiency may be broadly conserved.
Together, these studies show that topological flexibility in operons, DNA, nucleoid, protein structures, and the transcription network shapes how bacteria reorganize their physiology under stress. By tracing how these layers interact during different perturbations, this thesis offers a combined view of how bacterial cells interpret and integrate complex environmental cues.
Using Escherichia coli as our model organism, we examined how regulatory topology influences genome-wide adaptation during bacterial stress response. First, we investigated operon topology and how it affects transcriptional responses to stresses involving antibiotics and starvation. By combining transcriptomics, flow cytometry, and synthetic promoter constructs, we show that internal promoters within operons are positioned and tuned in ways that mitigate the transcriptional losses caused by premature transcriptional termination. These losses are further amplified by topological factors such as DNA supercoiling and collisions between elongating and promoter-bound RNA polymerases. Consistent with this, comparative analyses across evolutionarily distant bacteria indicate that similar operon-level transcriptional responses are broadly conserved.
Next, we explored transcription factor network (TFN) dynamics by constructing a library of fluorescent reporters for 16 global regulators, which collectively account ~30% of the E. Coli network topology. These constructs capture promoter-level transcription rates with high sensitivity and specificity under exponential, stationary, weak, and strong stress conditions. The reporters reveal substantial single-cell variability in global regulator (GR) activity and provide a quantitative tool to map the order, timing, and hierarchy of TFN activation during stress.
Finally, we examined how DNA structure, protein conformational flexibility, metabolic and regulatory networks contribute to adaptation under concurrent temperature and antibiotic stresses. We find that during combined exposure, transcriptomes collapse toward temperature-defined states. This dominance arises from topological constraints on nucleoid, ATP-dependent enzymatic activity, induction of global regulatory networks, and the conformational flexibility of antibiotic-target complexes. Cross-species simulations and phylogenetic comparisons suggest that temperature-induced changes in antibiotic efficiency may be broadly conserved.
Together, these studies show that topological flexibility in operons, DNA, nucleoid, protein structures, and the transcription network shapes how bacteria reorganize their physiology under stress. By tracing how these layers interact during different perturbations, this thesis offers a combined view of how bacterial cells interpret and integrate complex environmental cues.
Kokoelmat
- Väitöskirjat [5346]