Loss of SeqA confers low-level fluoroquinolone resistance through transcriptional reprogramming and RpoS dependence in <i>E. coli</i>

Amir Faraz; Nuha Abeer Khan; Deepak Kumar Singh; Hamna Syed; Mohan C. Joshi; Amir Faraz; Nuha Abeer Khan; Deepak Kumar Singh; Hamna Syed; Mohan C. Joshi

doi:10.3934/microbiol.2025047

AIMS Microbiology

2025, Volume 11, Issue 4: 1079-1100. doi: 10.3934/microbiol.2025047

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Research article

Loss of SeqA confers low-level fluoroquinolone resistance through transcriptional reprogramming and RpoS dependence in E. coli

Multidisciplinary Centre for Advanced Research and Studies (MCARS), Jamia Millia Islamia, New Delhi, India-110025

Received: 26 August 2025 Revised: 13 December 2025 Accepted: 18 December 2025 Published: 24 December 2025

SeqA is a key regulator of DNA replication initiation and chromosome cohesion in Escherichia coli. Loss of SeqA causes replication asynchrony, segregation defects, and growth delay, but its role in antibiotic susceptibility has remained unclear. Fluoroquinolones (FQs), which directly target bacterial DNA gyrase and topoisomerase IV to generate double-strand breaks (DSBs), provide a useful system to probe how chromosomal organization influences antibiotic response. In this study, we investigated whether SeqA loss alters sensitivity to FQs compared to antibiotics with non-DNA targets. MIC and MBC assays revealed that ΔseqA cells exhibit a specific low-level resistance to FQs, with ~1.5-fold higher inhibitory and bactericidal thresholds while retaining wildtype sensitivity to β-lactams and aminoglycosides. Using MuGam-GFP and RecA-GFP reporters, we showed that ΔseqA cells had fewer DSBs and mount an attenuated SOS response at wildtype MIC levels, enabling survival at otherwise lethal doses. Complementation restored wildtype sensitivity, confirming SeqA's direct involvement. Importantly, resistance was abolished in ΔseqA-rpoS double mutants and upon sub-MIC rifampicin treatment, demonstrating that RpoS-dependent transcriptional reprogramming underlies this phenotype. This suggested that ΔseqA strains acquire resistance through an RpoS-dependent regulatory effect that likely involves broad transcriptional reprogramming that underlies this phenotype. Together, these results showed that loss of SeqA alters chromosome organization in a way that lowers fluoroquinolone-induced DNA damage and enables RpoS-dependent low-level resistance.
- SeqA,
- Escherichia coli,
- Fluoroquinolones (FQs),
- antibiotic resistance,
- replication initiation,
- DNA double-strand breaks (DSB),
- SOS response,
- RpoS
Citation: Amir Faraz, Nuha Abeer Khan, Deepak Kumar Singh, Hamna Syed, Mohan C. Joshi. Loss of SeqA confers low-level fluoroquinolone resistance through transcriptional reprogramming and RpoS dependence in E. coli[J]. AIMS Microbiology, 2025, 11(4): 1079-1100. doi: 10.3934/microbiol.2025047

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Abstract

SeqA is a key regulator of DNA replication initiation and chromosome cohesion in Escherichia coli. Loss of SeqA causes replication asynchrony, segregation defects, and growth delay, but its role in antibiotic susceptibility has remained unclear. Fluoroquinolones (FQs), which directly target bacterial DNA gyrase and topoisomerase IV to generate double-strand breaks (DSBs), provide a useful system to probe how chromosomal organization influences antibiotic response. In this study, we investigated whether SeqA loss alters sensitivity to FQs compared to antibiotics with non-DNA targets. MIC and MBC assays revealed that ΔseqA cells exhibit a specific low-level resistance to FQs, with ~1.5-fold higher inhibitory and bactericidal thresholds while retaining wildtype sensitivity to β-lactams and aminoglycosides. Using MuGam-GFP and RecA-GFP reporters, we showed that ΔseqA cells had fewer DSBs and mount an attenuated SOS response at wildtype MIC levels, enabling survival at otherwise lethal doses. Complementation restored wildtype sensitivity, confirming SeqA's direct involvement. Importantly, resistance was abolished in ΔseqA-rpoS double mutants and upon sub-MIC rifampicin treatment, demonstrating that RpoS-dependent transcriptional reprogramming underlies this phenotype. This suggested that ΔseqA strains acquire resistance through an RpoS-dependent regulatory effect that likely involves broad transcriptional reprogramming that underlies this phenotype. Together, these results showed that loss of SeqA alters chromosome organization in a way that lowers fluoroquinolone-induced DNA damage and enables RpoS-dependent low-level resistance.

Declaration of competing interest

The authors declare that they have no known competing financial or personal interests that could have appeared to influence the work reported in this paper.

Authors contribution

Conceptualization: [MCJ & AF] Methodology: [MCJ & AF] Formal analysis and investigation: [MCJ, AF, NAK, DKS & HS] Writing - original draft preparation: [AF] Writing - review and editing: [MCJ, AF, NAK, DKS] Funding acquisition: [MCJ] Supervision: [MCJ]

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