ppGpp and RNA-polymerase backtracking guide antibiotic-induced mutable gambler cells

• DOI: 10.1016/j.molcel.2023.03.003
• Publication Date: 2023-03-24T14:43:23Z
• Authors: Yin Zhai; P.J. Minnick; John P. Pribis; Libertad Garcia-V...; P.J. Hastings; Christophe Herman; Susan M. Rosenberg
• Keywords: 0301 basic medicine; 570; antibiotic resistance; Medical Sciences; Biophysics; 610; Guanosine Tetraphosphate; Biochemistry; Biomedical Informatics; 03 medical and health sciences; ppGpp; Ciprofloxacin; evolution; Medical Specialties; Medicine and Health Sciences; Escherichia coli; stress-induced mutagenesis; fluoroquinolones; Biology; reactive oxygen species; 0303 health sciences; Escherichia coli Proteins; Bacterial; Life Sciences; stringent response; DNA-Directed RNA Polymerases; DNA; Gene Expression Regulation, Bacterial; mutations; mutagenic break repair; Anti-Bacterial Agents; Gene Expression Regulation; general stress response; and Structural Biology; RNA

SUMMARYAntibiotics can induce mutations that cause antibiotic resistance, triggered by stress responses. The identities of the stress-response activators reveal environmental cues that elicit mutagenesis, and are weak links in mutagenesis networks, inhibition of which could slow evolution of resistance during antibiotic therapies. Despite pivotal importance, few identities and fewer functions of stress responses in mutagenesis are clear. Here, we identify the stringent starvation response in fluoroquinolone-antibiotic ciprofloxacin (stress)-induced mutagenesis. We show its role in transient differentiation of a mutable “gambler” cell subpopulation. Stringent activity is induced by reactive oxygen and upregulates two small (s)RNAs that induce the general stress response, which allows mutagenic DNA-break repair. Surprisingly, RNA polymerase and response-activator nucleotide (p)ppGpp promote ciprofloxacin-induced DNA-damage signaling. We propose a model for their regulation of DNA-damage processing in transcribed regions. The data demonstrate a critical node in ciprofloxacin-induced mutagenesis, imply RNA-polymerase regulation of DNA-break repair, and identify promising targets for resistance-resisting drugs.