RNA-Mediated cis Regulation in Acinetobacter baumannii Modulates Stress-Induced Phenotypic Variation

In the nosocomial opportunistic pathogenAcinetobacter baumannii , RecA-dependent mutagenesis, which causes antibiotic resistance acquisition, is linked to the DNA damage response (DDR). Notably, unlike theEscherichia coli paradigm,recA and DDR gene expression inA. baumannii is bimodal. Namely, there is phenotypic variation upon DNA damage, which may provide a bet-hedging strategy for survival. Thus, understandingrecA gene regulation is key to elucidate the yet unknown DDR regulation inA. baumannii . Here, we identify a structured 5′ untranslated region (UTR) in therecA transcript which serves as acis -regulatory element. We show that a predicted stem-loop structure in this 5′ UTR affects mRNA half-life and underlies bimodal gene expression and thus phenotypic variation in response to ciprofloxacin treatment. We furthermore show that the stem-loop structure of therecA 5′ UTR influences intracellular RecA protein levels and,in vivo , impairing the formation of the stem-loop structure of therecA 5′ UTR lowers cell survival of UV treatment and decreases rifampin resistance acquisition from DNA damage-induced mutagenesis. We hypothesize that the 5′ UTR allows for stablerecA transcripts during stress, including antibiotic treatment, enabling cells to maintain suitable RecA levels for survival. This innovative strategy to regulate the DDR inA. baumannii may contribute to its success as a pathogen.IMPORTANCE Acinetobacter baumannii is an opportunistic pathogen quickly gaining antibiotic resistances. Mutagenesis and antibiotic resistance acquisition are linked to the DNA damage response (DDR). However, how the DDR is regulated inA. baumannii remains unknown, since unlike most bacteria,A. baumannii does not follow the regulation of theEscherichia coli paradigm. In this study, we have started to uncover the mechanisms regulating the novelA. baumannii DDR. We have found that acis -acting 5′ UTR regulatesrecA transcript stability, RecA protein levels, and DNA damage-induced phenotypic variation. Though 5′ UTRs are known to provide stability to transcripts in bacteria, this is the first example in which it regulates a bimodal DDR response throughrecA transcript stabilization, potentially enabling cells to have enough RecA for survival and genetic variability.