Genetic analysis of epistasis between nucleotide excision repair and homologous recombination in the recovery of persisters after fluoroquinolone treatment
- 1Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- 2Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
- 3Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey, United States of America
Abstract
Stationary-phase cultures contain high abundances of persisters, which are bacterial cells that are hyper-tolerant to antibiotics due to phenotypic reasons. Fluoroquinolones (FQs) are one of the most effective antibiotic classes for the treatment of non-growing bacteria, such as those found in stationary-phase cultures, and persisters in those populations have been found to survive FQ treatment by repairing the DNA damage caused by the antibiotic rather than by avoiding damage through inactivity. Interestingly, previous work demonstrated that transient growth inhibition after the conclusion of FQ treatment significantly increased persister levels from stationary-phase Escherichia coli populations if recA, a mediator of homologous recombination (HR), or uvrD, a component of nucleotide excision repair (NER), were present. Here, we sought to identify additional epistatic interaction partners in that persister recovery network by deleting DNA repair enzymes known to interact with RecA or UvrD. We found that uvrA, uvrB, and mfd also epistatically interact with recA in FQ persister recovery, whereas recB and recC are additional epistatic interaction partners of uvrD. While these results indicated that HR and NER can contribute to persister recovery, different combinations of genetic mutants suggested that the phenomenon is more nuanced than compensation for loss of one repair pathway by another. Specifically, loss of recA had farther reaching epistatic consequences than loss of other HR genes, and loss of uvrD had a greater impact on the network than any other NER gene. Delving deeper into the roles of RecA and UvrD, we found that the recombination function of RecA, via RecA(N304D), and helicase function of UvrD, via UvrD(R284A), were required for their participation in FQ persister recovery. Collectively, the data presented here deepen understanding of the roles of HR and NER machinery in the recovery FQ persisters and further emphasize the important roles of RecA and UvrD in this phenomenon. Author summary: Persisters are rare phenotypic variants that survive antibiotic treatments that kill the vast majority of cells in cultures, and evidence has accumulated to support their role in chronic and recurrent infections. Persisters are abundant in populations where nutrients have been exhausted, such as stationary-phase cultures, and FQs are one of the few antibiotic classes that remain efficacious against such populations. Previous work found that transient growth inhibition after FQ treatment increased the abundance of persisters from stationary-phase E. coli populations by providing time for bacteria to repair FQ-induced DNA damage before resuming growth. Further, an epistasis between recA (a mediator of homologous recombination) and uvrD (a participant in nucleotide excision repair) was uncovered in the phenomenon. Here we adopted a genetic approach to identify additional members of this epistatic network by focusing on known interaction partners of RecA and UvrD. We found that uvrA, uvrB, and mfd also epistatically interact with recA, whereas recB and recC are additional epistatic interaction partners of uvrD. Additional analyses revealed the central roles of recA and uvrD in this epistatic network that has the capacity to reduce the efficacy of FQs by up to an order of magnitude.
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BibTeX
@article{sotoechevarria2026genetic,
title = {{Genetic analysis of epistasis between nucleotide excision repair and homologous recombination in the recovery of persisters after fluoroquinolone treatment}},
author = {Nashaly Soto-Echevarria and Annabel S. Lemma and Mark P. Brynildsen},
journal = {PLOS Genetics},
year = {2026},
month = sep,
doi = {10.1371/journal.pgen.1012305},
url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012305},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genetic analysis of epistasis between nucleotide excision repair and homologous recombination in the recovery of persisters after fluoroquinolone treatment
AU - Nashaly Soto-Echevarria
AU - Annabel S. Lemma
AU - Mark P. Brynildsen
PY - 2026
DA - 2026/09/21
JO - PLOS Genetics
DO - 10.1371/journal.pgen.1012305
UR - https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012305
AB - Stationary-phase cultures contain high abundances of persisters, which are bacterial cells that are hyper-tolerant to antibiotics due to phenotypic reasons. Fluoroquinolones (FQs) are one of the most effective antibiotic classes for the treatment of non-growing bacteria, such as those found in stationary-phase cultures, and persisters in those populations have been found to survive FQ treatment by repairing the DNA damage caused by the antibiotic rather than by avoiding damage through inactivity. Interestingly, previous work demonstrated that transient growth inhibition after the conclusion of FQ treatment significantly increased persister levels from stationary-phase Escherichia coli populations if recA, a mediator of homologous recombination (HR), or uvrD, a component of nucleotide excision repair (NER), were present. Here, we sought to identify additional epistatic interaction partners in that persister recovery network by deleting DNA repair enzymes known to interact with RecA or UvrD. We found that uvrA, uvrB, and mfd also epistatically interact with recA in FQ persister recovery, whereas recB and recC are additional epistatic interaction partners of uvrD. While these results indicated that HR and NER can contribute to persister recovery, different combinations of genetic mutants suggested that the phenomenon is more nuanced than compensation for loss of one repair pathway by another. Specifically, loss of recA had farther reaching epistatic consequences than loss of other HR genes, and loss of uvrD had a greater impact on the network than any other NER gene. Delving deeper into the roles of RecA and UvrD, we found that the recombination function of RecA, via RecA(N304D), and helicase function of UvrD, via UvrD(R284A), were required for their participation in FQ persister recovery. Collectively, the data presented here deepen understanding of the roles of HR and NER machinery in the recovery FQ persisters and further emphasize the important roles of RecA and UvrD in this phenomenon. Author summary: Persisters are rare phenotypic variants that survive antibiotic treatments that kill the vast majority of cells in cultures, and evidence has accumulated to support their role in chronic and recurrent infections. Persisters are abundant in populations where nutrients have been exhausted, such as stationary-phase cultures, and FQs are one of the few antibiotic classes that remain efficacious against such populations. Previous work found that transient growth inhibition after FQ treatment increased the abundance of persisters from stationary-phase E. coli populations by providing time for bacteria to repair FQ-induced DNA damage before resuming growth. Further, an epistasis between recA (a mediator of homologous recombination) and uvrD (a participant in nucleotide excision repair) was uncovered in the phenomenon. Here we adopted a genetic approach to identify additional members of this epistatic network by focusing on known interaction partners of RecA and UvrD. We found that uvrA, uvrB, and mfd also epistatically interact with recA, whereas recB and recC are additional epistatic interaction partners of uvrD. Additional analyses revealed the central roles of recA and uvrD in this epistatic network that has the capacity to reduce the efficacy of FQs by up to an order of magnitude.
SN - 1553-7404
ER -