Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in Starving Escherichia coli.
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 F' plasmid maintenance, allowing MBR to be measured in an F'-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.
Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, 77030 Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030.
Jessica M
JM
Moore
Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030.
David
D
Magnan
Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 Undergraduate Program on Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, 62210, Morelos, Mexico.
Ana K
AK
Mojica
Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, 77030 Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030.
María Angélica Bravo
MA
Núñez
Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, 77030.
David
D
Bates
Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, 77030 Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, 77030.
Susan M
SM
Rosenberg
Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 hastings@bcm.edu.
P J
PJ
Hastings
D002876:Chromosomes, Bacterial / Q000378:metabolism; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D009154:Mutation; D013014:SOS Response, Genetics
D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins
double-strand break repair; evolution; mutagenesis; nucleoid-associated proteins (NAPs); stress response