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ABSTRACT The mutagenicity of DNA double-strand break repair in Escherichia coli is controlled by DNA-damage (SOS) and general (RpoS) stress responses, which let error-prone DNA polymerases participate, potentially accelerating evolution during stress. Either base substitutions and indels or genome rearrangements result. Here we discovered that most small basic proteins that compact the genome, nucleoid-associated proteins (NAPs), promote or inhibit mutagenic break repair (MBR) via different routes. Of 15 NAPs, H-NS, Fis, CspE, and CbpA were required for MBR; Dps inhibited MBR; StpA and Hha did neither; and five others were characterized previously. Three essential genes were not tested. Using multiple tests, we found the following: First, Dps, which reduces reactive oxygen species (ROS), inhibited MBR, implicating ROS in MBR. Second, CbpA promoted F9 plasmid maintenance, allowing MBR to be measured in an F9-based assay. Third, Fis was required for activation of the SOS DNA-damage response and could be substituted in MBR by SOS-induced levels of DinB error-prone DNA polymerase. Thus, Fis promoted MBR by allowing SOS activation. Fourth, H-NS represses ROS detoxifier sodB and was substituted in MBR by deletion of sodB, which was not otherwise mutagenic. We conclude that normal ROS levels promote MBR and that H-NS promotes MBR by maintaining ROS. CspE positively regulates RpoS, which is required for MBR. Four of five previously characterized NAPs promoted stress responses that enhance MBR. Hence, most NAPs affect MBR, the majority via regulatory functions. The data show that a total of six NAPs promote MBR by regulating stress responses, indicating the importance of nucleoid structure and function to the regulation of MBR and of coupling mutagenesis to stress, creating genetic diversity responsively.
KEYWORDS double-strand break repair; evolution; mutagenesis; nucleoid-associated proteins (NAPs); stress response
IN Escherichia coli, the structure of the bacterial chromosome or nucleoid is governed by the action of small, abundant DNA-binding nucleoid-associated proteins (NAPs) (Ali Azam et al. 1999). NAPs bind dynamically to the genome both sequence specifically and sequence nonspecifically, causing a variety of genomic conformations (Azam et al. 2000). Through this action, several NAPs also act as global transcriptional regulators, with some of their regulons containing hundreds of genes (Oberto et al. 2009; Kahramanoglou et al. 2011; Chib and Mahadevan 2012). There are 15 NAPs: Hfq, IHF-A and IHF-B (which...