Identifying bacterial DNA repair requirements enabling stable genetic inheritance during bidirectional replication fork collapse

About the Project

DNA replication termination is critical to ensure stable genome maintenance, thereby preventing cellular ageing. In eukaryotes, defective termination is a genetic hallmark of cancer, whereby mutations in regulatory genes can contribute to genome degeneration, leading to metastasis and/or cell death. However, dynamics of the bacterial chromosome during termination are more complex, where replication fork trap systems, restart of DNA synthesis, and redundant repair processes may play distinct roles to regulate genetic inheritance. Critically, the field lacked methodology to disentangle genetic complexity and fundamental regulation of termination mechanisms in prokaryotes.

To explore this question, the Winterhalter lab recently published an innovative approach based on the CRISPR/Cas system to introduce unique DNA breaks at a defined position on the bacterial chromosome. We used this technique to identify important genes involved in DNA repair and surprisingly, only a minimal set of recombination factors were involved in replication fork repair. Further characterisation and recent data suggest that alternative, potentially error-prone processes become activated when two bacterial replication forks converge, akin to repair processes observed in eukaryotes. Excitingly, our ability to engineer artificial sites to reprogram replication termination in bacteria now enables us to interrogate the critical repair processes required to process the byproducts of a bidirectional replication fork collapse.

This multidisciplinary project will employ model laboratory strains of Bacillus subtilis and Escherichia coli,species that mechanistically differ in regulation of replication termination. First, you will employ genetics to engineer a set of bacterial strains that promote site-specific bidirectional replication fork collapse, and identify replication conflicts by marker frequency analyses. You will then characterise chromosome distribution at a single cell level via fluorescence microscopy, and employ immunoprecipitation-based approaches to build a molecular map of the repair complexes involved in DNA processing. Finally, you will employ biochemistry to purify and reconstitute the core processes driving DNA repair in vitroduring bidirectional replication fork collapse. Shared work experience between the Winterhalter and Murray labs (Newcastle University) will enable you to discover collaborative research and development in inclusive and vibrant environments. Our team will train you in techniques that are broadly applicable in fundamental and applied biosciences including bacterial genetics, single cell microscopy and biochemical characterisation of nucleoprotein complexes. This studentship will equip you with a transferrable skillset and valuable experience in fundamental microbiology. Importantly, your work on replication fork collapse may pave the way towards the development of alternative antimicrobials targeting bacterial termination mechanisms.

Funding

Students who have, or are expecting to attain, at least an upper second-class honours degree (or equivalent) in a relevant subject, are invited to apply. Funding is available for Home (UK) students to cover tuition fees, a tax-free stipend at the UKRI rate (indicative amount in year 1 in 2026-27, £21,805) and research costs, for four years. Applicants normally required to cover International fees will have to cover the difference between the Home and the International tuition fee rates. There is no additional funding available to cover NHS Immigration Health Surcharge (IHS) costs, visa costs, flights etc.

Funding for this studentship is awarded on a competitive basis and is not guaranteed; availability will depend on the outcome of the selection process and subject to final approval by the University.