DNA breaks-mediated cost reveals RNase HI as a new target for selectively eliminating antibiotic resistance

Roberto Balbontín; Nelson Frazão; Isabel Gordo

Both transcription-translation uncoupling and replication-transcription conflicts lead to increased formation of R-loops, which cause DNA breaks (42,59) and exacerbate replicationtranscription conflicts themselves by impairing replication fork progression (60) . We thus reasoned that depleting RNase HI function, which specifically degrades R-loops (61), should lead to increased DNA breaks and greater costs of Rif R and Str R . Accordingly, both DNA breaks and the cost of resistance are greatly exacerbated in the ΔrnhA background ( Figure 4A , Table 1 , Figure S3 , Figure S4A ). Conversely, mild overproduction of RNase HI can ameliorate both phenotypes in a subset of mutants ( Figure S5 ); however, strong overproduction is toxic for the cell (62, 63) , irrespective of its genotype ( Figure S6 ).