http://bura.brunel.ac.uk/handle/2438/32874 2026-04-26T00:55:07Z http://bura.brunel.ac.uk/handle/2438/33186 Title: Investigating replication fork blocks, replication-transcription conflicts and replication restart dynamics in Escherichia coli Authors: Peros, Stelinda Abstract: DNA replication is essential for genome stability, but it is constantly jeopardized by various obstacles such as nucleoprotein complexes and transcription–replication conflicts. If not properly resolved, these impediments lead to replication fork collapse, genomic instability, and even cell death. This thesis investigates how Escherichia coli preserves its replication integrity using three experimental systems: site-specific protein– DNA blockades, engineered replication–transcription conflicts, and chemical stress induced by saccharin exposure. These studies were supported by the development of an automated bioimage informatics pipeline, utilizing deep-learning segmentation to enable high-throughput quantitative analysis of cellular morphology and SOS-induced stress phenotypes in live-cell time-lapse microscopy. Using a novel inducible fork-block model, I demonstrate that the PriA–PriB– DnaT pathway is the primary restart mechanism at nucleoprotein obstacles, with PriA helicase activity being essential for efficient replication restart. Surprisingly, when large tandem repeats were placed on the opposite replichore, PriC rather than PriB played the dominant role, raising the possibility that restart pathway usage is influenced by obstacle size or chromosomal context. Replication–transcription conflicts, generated by introducing an ectopic origin of replication (oriZ), similarly required PriA helicase and PriB for efficient fork restart. In their absence, cells displayed severe filamentation, heterogeneous stress phenotypes, and elevated Cas1–Cas2 foci. To further define the nature of these collisions, I utilized an alternative origin (oriX); the comparison between head-on and co-directional orientations confirmed that cellular pathology was specifically conflict- dependent. Genetic suppression with an RNA polymerase–destabilizing mutation confirmed that these defects stem directly from transcriptional collisions rather than indirect effects. Finally, I show that saccharin, a widely used artificial sweetener, induces replication stress in E. coli, with PriB-deficient cells exhibiting pronounced defects and loss of viability. These findings highlight how dietary compounds may disrupt gut microbial physiology. Collectively, this work establishes PriA helicase as a central player in replication restart and a promising antibacterial target. Since stalled fork rescue is also critical in cancer cells, these results also provide conceptual bridges between bacterial DNA replication and oncogene-induced replication stress, opening avenues for both antimicrobial and cancer therapeutic development. Description: This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London 2025-01-01T00:00:00Z http://bura.brunel.ac.uk/handle/2438/32769 Title: Novel memory phenotype Tfh cells arise without overt antigen stimulation and are important for adaptive immune responses against viral infection Authors: Busharat, Zabreen Abstract: Pathogen-induced memory Tfh cells exert a Tfh effector response during reinfection, regulating the generation of high-affinity antibodies. Here, we define novel memory-phenotype Tfh cells which are generated from naïve T cells under homeostatic conditions. These MP Tfh cells are phenotypically and functionally similar to pathogen-induced Tfh cells. MP Tfh cells can be defined by Tfh cell specific markers, CXCR5, BCL6, and PD-1, and markers of pathogen-induced long lived Tfh cells, FR4. T-bethigh MP T cells exert an innate-like Th1 response against viral infections. The transcription factor EGR2 is a repressor of T-bet function, and we found that MP Tfh cells are distinct from T-bethigh MP T cells but express EGR2 highly. Previously, we found Egr2 is required for MP T cell homeostasis and inflammation. Here, we observed that, in Egr2/3-/- CD4+ MP T cells, MP Tfh cell development is impaired. FR4+ EGR2 + MP T cells upregulate genes related to homeostatic proliferation, Tfh cell development and metabolic pathways of pathogen-induced memory Tfh cells. MP Tfh cells can exert an adaptive function by regulating B cell-mediated IgG production in vitro whereas MP Tfr cells are involved in suppressing MP Tfh cell function, thereby preventing excessive inflammation. In vivo, MP Tfh cells support germinal centre formation and induce neutralising antibody production after infection with vaccinia virus. Thus, MP Tfh cells with similar characteristics to pathogen-induced memory Tfh cells are developed in absence of environmental antigens and to date are the only CD4+ MP T cell subset associated with an adaptive immune response against viral infection. Description: This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London 2025-01-01T00:00:00Z