Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

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.

The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment

“…Some of the phenotypic effects due to hfq mutation may indeed be due to defects in DNA-related processes; for instance, slow-down of growth and filamentation are signs of replication misregulation. Sensitivity to mutagens could also indicate problems in DNA repair [4,25].…”

Mutation and Recombination Rates Vary Across Bacterial Chromosome

“…Study by Williams and Foster [74] demonstrated that HU is involved in the occurrence of Lac + revertants in E. coli FC40, possibly helping to channel recombination intermediates for resolution via a RuvABC-dependent mutagenic pathway instead a RecG-dependent non-mutagenic pathway. In the MBR examined in E. coli FC40 and its derivatives, only HU directly promotes homologous recombination, whereas other NAPs (Fis, H-NS, CspE, CspC, CbpA, Lrp, Hfq and IHF) participate in the regulation of mutagenic processes [75,76]. Using multiple in vivo tests, Moore and colleagues [77] observed that most studied NAPs promote MBR, but via different mechanisms [77].…”

“…Among the studied NAPs, DNA binding protein from starved cells (Dps) has been the sole inhibitor of mutagenesis in the MBR pathway [75], and has had no effect on the pattern of mutation rate in the MA-WGS experiments [43]. Dps is the most abundant protein component of the nucleoid in stationary phase cells that compacts and co-crystalizes with DNA and protects DNA from reactive oxygen species [15].…”

Oxygen and RNA in stress-induced mutation

“…However, while studying the mutational roles of proteins that attach to DNA in E. coli , we found correlations between mutagenesis and the presence of reactive oxygen species (ROS) (Moore et al 2015). Specifically, H-NS, a global gene regulator (repressor), is required for MBR via its repression of SodB, an antioxidant enzyme that reduces levels of superoxide.…”