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

Antibiotic resistance is a global health threat and often results from new mutations. Antibiotics can induce mutations via mechanisms activated by stress responses, which both reveal environmental cues of mutagenesis and are weak links in mutagenesis networks. Network inhibition could slow the evolution of resistance during antibiotic therapies. Despite its pivotal importance, few identities and fewer functions of stress responses in mutagenesis are clear. Here, we identify the Escherichia coli stringent starvation response in fluoroquinolone-antibiotic ciprofloxacin-induced mutagenesis. Binding of response-activator ppGpp to RNA polymerase (RNAP) at two sites leads to an antibiotic-induced mutable gambler-cell subpopulation. Each activates a stress response required for mutagenic DNA-break repair: surprisingly, ppGpp-site-1-RNAP triggers the DNA-damage response, and ppGpp-site-2-RNAP induces σS-response activity. We propose that RNAP regulates DNA-damage processing in transcribed regions. The data demonstrate a critical node in ciprofloxacin-induced mutagenesis, imply RNAP-regulation of DNA-break repair, and identify promising targets for resistance-resisting drugs. [Display omitted] •Stringent starvation response leads to mutable gambler-cell subpopulation•RNA polymerase (RNAP)-(p)ppGpp-site-1 triggers the SOS DNA-damage response•Antibiotic → SOS → reactive oxygen+ cells → stringent-on cells → σS response-on gamblers•(p)ppGpp-RNAPs play two roles: backtracking/SOS, then inducing sRNAs → σS activity Binding of starvation-response activator ppGpp to RNA polymerase (RNAP) at two sites leads to an antibiotic-induced mutable gambler-cell subpopulation. Each activates a stress response required for mutagenic DNA-break repair: backtracked RNAP-ppGpp-site-1 triggers SOS, and ppGpp-site-2-RNAP induces σS-response activity. The two cause mutations, some of which confer resistance to new antibiotics.