SOS induction and mutagenesis by dnaQ missense alleles in wild type cells

Mutational Signatures in Wild Type Escherichia coli Strains Reveal Predominance of DNA Polymerase Errors

While mutational processes operating in the Escherichia coli genome have been revealed by multiple laboratory experiments, the contribution of these processes to accumulation of bacterial polymorphism and evolution in natural environments is unknown. To address this question, we reconstruct signatures of distinct mutational processes from experimental data on E. coli hypermutators, and ask how these processes contribute to differences between naturally occurring E. coli strains. We show that both mutations accumulated in the course of evolution of wild-type strains in nature and in the lab-grown nonmutator laboratory strains are explained predominantly by the low fidelity of DNA polymerases II and III. By contrast, contributions specific to disruption of DNA repair systems cannot be detected, suggesting that temporary accelerations of mutagenesis associated with such disruptions are unimportant for within-species evolution. These observations demonstrate that accumulation of diversity in bacterial strains in nature is predominantly associated with errors of DNA polymerases.

The Spectrum of Replication Errors in the Absence of Error Correction Assayed Across the Whole Genome of Escherichia coli

When the DNA polymerase that replicates the Escherichia coli chromosome, DNA polymerase III, makes an error, there are two primary defenses against mutation: proofreading by the ϵ subunit of the holoenzyme and mismatch repair. In proofreading-deficient strains, mismatch repair is partially saturated and the cell's response to DNA damage, the SOS response, may be partially induced. To investigate the nature of replication errors, we used mutation accumulation experiments and whole-genome sequencing to determine mutation rates and mutational spectra across the entire chromosome of strains deficient in proofreading, mismatch repair, and the SOS response. We report that a proofreading-deficient strain has a mutation rate 4000-fold greater than wild-type strains. While the SOS response may be induced in these cells, it does not contribute to the mutational load. Inactivating mismatch repair in a proofreading-deficient strain increases the mutation rate another 1.5-fold. DNA polymerase has a bias for converting G:C to A:T base pairs, but proofreading reduces the impact of these mutations, helping to maintain the genomic G:C content. These findings give an unprecedented view of how polymerase and error-correction pathways work together to maintain E. coli's low mutation rate of 1 per 1000 generations.

Comparative evaluation of antimutagenicity of commonly consumed fruits and activity-guided identification of bioactive principles from the most potent fruit, Java plum (Syzygium cumini)

Commonly consumed fruits showed remarkable variation in antimutagenicity when assayed by E. coli rifampicin resistance assay, and Java plum (Syzygium cumini) was found to be one of the most potent fruits. Its anthocyanins contributed maximally to the observed antimutagenicity and resolved into three distinct bands in HPTLC. Although these bands displayed similar antioxidant capacity, the band at R(f) 0.22 was the most antimutagenic and resolved into two peaks in HPLC. The second peak (t(R) 3.8 min) displayed a strong and broad spectrum antimutagenicity and was identified as petunidin-3,5-diglucoside by analysis of its molecular ion and fragmentation pattern by ESI-MS/MS. The presence of glucose moiety was confirmed by TLC analysis of acid-hydrolyzed products. This purified anthocyanin was found to suppress mutagenic SOS DNA repair process in E. coli and thus indicated suppression of the error-prone DNA repair pathway as one of the major mechanisms of antimutagenicity of this fruit.

Potential roles for DNA replication and repair functions in cell killing by streptomycin

The aminoglycoside streptomycin binds to ribosomes to promote mistranslation and eventual inhibition of translation. Streptomycin kills bacteria, whereas many other non-aminoglycoside inhibitors of translation do not. Because mistranslation is now known to affect DNA replication, we asked if hydroxyurea, a specific inhibitor of DNA synthesis, affects killing, and find that hydroxyurea significantly attenuates killing by streptomycin. We find that the hydroxyl radical scavengers d-mannitol and thiourea have either no effect or only a modest protective effect. The iron chelator 2,2'-dipyridyl eliminated killing by streptomycin, but further investigation revealed that it blocks streptomycin uptake. Prior treatment of cells with low-levels of methyl methanesulfonate to induce the adaptive response to alkylation leads to a significant attenuation of killing, which, together with the hydroxyurea effect, suggests roles for DNA replication and repair functions in cell killing by streptomycin.