New Nucleic Acids Research paper: Exploring the genetic landscape of ciprofloxacin-induced DNA supercompaction in Escherichia coli
Work by Krister Vikedal from the Bacterial Defense Systems and Antimicrobial Resistance Group led by James Booth and Emily Helgesen at the Department of Microbiology shows that combining high-content imaging with machine learning is a powerful, scalable way to map how bacterial genes shape chromosome organization and DNA damage responses. The modular nature of the developed method means it can readily be extended to other gene libraries, stress conditions, reporters, or bacterial species. These insights bring us a step closer to understanding — and ultimately combating — antibiotic resistance.
Summary from the authors:
Fluoroquinolone antibiotics like ciprofloxacin are widely used to treat bacterial infections, but resistance is rising. Ciprofloxacin works by blocking enzymes that copy bacterial DNA, causing many dangerous breaks in the chromosome. In Escherichia coli, this not only switches on an emergency DNA repair program called the SOS response, it also makes the chromosome collapse into a tightly packed ball, a process our lab calls “DNA supercompaction”.
DNA supercompaction
When DNA is damaged, the protein RecA senses exposed DNA and inactivates LexA, lifting repression of many SOS genes. This boosts production of repair factors, including RecN, a chromosome-organizing protein that becomes one of the most abundant proteins during the SOS response. Researchers in the Bacterial Defense Systems and Antimicrobial Resistance Group at OUS previously showed that severe ciprofloxacin damage drives the nucleoid through a stepwise reorganization, ending in a dense midcell mass. This final “supercompacted” state depends on both RecA and RecN. An earlier intermediate shape still appears when these proteins are missing, hinting that other, unknown genes are involved.
Screening mutants with imaging and AI
To find these missing players, we screened nearly 4,000 E. coli strains from the Keio deletion library and additional in-house strains. Using high-content fluorescence imaging and machine learning to classify DNA shapes after ciprofloxacin treatment, we identified 15 strains with impaired DNA supercompaction.
Strains lacking known DNA recombination repair genes showed the strongest defects, confirming their central role. Others lacked genes not previously linked to DNA repair, such as yaiW, which encodes a membrane-associated protein, and showed milder, more heterogeneous effects.
New genes, new tools
Follow-up experiments revealed that these “non-repair” genes can subtly alter where RecN sits on the chromosome, how much of it is produced, how strongly the SOS response is activated, and how well cells survive ciprofloxacin. This confirms RecA and RecN as primary drivers of DNA supercompaction but also uncovers additional genes that fine-tune the response.
More broadly, our work shows that combining high-content imaging with machine learning is a powerful, scalable way to map how bacterial genes shape chromosome organization and DNA damage responses. The modular nature of the developed method means it can readily be extended to other gene libraries, stress conditions, reporters, or bacterial species. These insights bring us a step closer to understanding — and ultimately combating — antibiotic resistance.
Links:
Link to the paper:
Vikedal K, Berges N, Riisnæs IMM, Ræder SB, Bjørnholt JV, Bjørås M, Skarstad K, Helgesen E, Booth JA (2026)
Exploring the genetic landscape of ciprofloxacin-induced DNA supercompaction in Escherichia coli
Nucleic Acids Res, 54 (12)
DOI 10.1093/nar/gkag573, PubMed 42328795
Related paper from 2025:
Vikedal K, Ræder SB, Riisnæs IMM, Bjørås M, Booth JA, Skarstad K, Helgesen E (2025)
RecN and RecA orchestrate an ordered DNA supercompaction response following ciprofloxacin-induced DNA damage in Escherichia coli
Nucleic Acids Res, 53 (10)
DOI 10.1093/nar/gkaf437, PubMed 40433982
Link to research group:
OUH - Bacterial Defense Systems and Antimicrobial Resistance Group, headed by James Booth and Emily Helgesen