The Small RNA GcvB Promotes Mutagenic Break Repair by Opposing the Membrane Stress Response

Microbes and human cells possess mechanisms of mutagenesis activated by stress responses. Stress-inducible mutagenesis mechanisms may provide important models for mutagenesis that drives host-pathogen interactions, antibiotic resistance, and possibly much of evolution generally. In Escherichia coli, repair of DNA double-strand breaks is switched to a mutagenic mode, using error-prone DNA polymerases, via the SOS DNA damage and general (σ(S)) stress responses. We investigated small RNA (sRNA) clients of Hfq, an RNA chaperone that promotes mutagenic break repair (MBR), and found that GcvB promotes MBR by allowing a robust σ(S) response, achieved via opposing the membrane stress (σ(E)) response. Cells that lack gcvB were MBR deficient and displayed reduced σ(S)-dependent transcription but not reduced σ(S) protein levels. The defects in MBR and σ(S)-dependent transcription in ΔgcvB cells were alleviated by artificially increasing σ(S) levels, implying that GcvB promotes mutagenesis by allowing a normal σ(S) response. ΔgcvB cells were highly induced for the σ(E) response, and blocking σ(E) response induction restored both mutagenesis and σ(S)-promoted transcription. We suggest that GcvB may promote the σ(S) response and mutagenesis indirectly, by promoting membrane integrity, which keeps σ(E) levels lower. At high levels, σ(E) might outcompete σ(S) for binding RNA polymerase and so reduce the σ(S) response and mutagenesis. The data show the delicate balance of stress response modulation of mutagenesis. IMPORTANCE Mutagenesis mechanisms upregulated by stress responses promote de novo antibiotic resistance and cross-resistance in bacteria, antifungal drug resistance in yeasts, and genome instability in cancer cells under hypoxic stress. This paper describes the role of a small RNA (sRNA) in promoting a stress-inducible-mutagenesis mechanism, mutagenic DNA break repair in Escherichia coli. The roles of many sRNAs in E. coli remain unknown. This study shows that ΔgcvB cells, which lack the GcvB sRNA, display a hyperactivated membrane stress response and reduced general stress response, possibly because of sigma factor competition for RNA polymerase. This results in a mutagenic break repair defect. The data illuminate a function of GcvB sRNA in opposing the membrane stress response, and thus indirectly upregulating mutagenesis.