On the role of dcm and vsr in Escherichia coli adaptive mutation

Abstract

Microorganisms rapidly adapt to non-lethal stress through mutations, a process central to microbial evolution. In this study, we investigate the molecular mechanism of adaptive mutagenesis in the bacterial strain Escherichia coli K-12 harboring a frameshift lac mutation. A non-random mutational spectrum, featuring a prominent − 1 bp deletion hot-spot is an intriguing unsolved phenomenon seen in the revertants of starving cells of this strain. The very-short-patch mismatch repair, a stationary-phase specific DNA repair pathway, has been hypothesized to create this hot-spot. To test this, we independently inactivated two main players of this pathway: dcm involved in DNA cytosine methylation and vsr encoding a sequence-specific DNA repair endonuclease. Contrary to the prediction of our hypothesis, the stationary-phase mutational spectra of Δdcm and Δvsr strains were indistinguishable from that of the wild-type strain, i.e., the frequency of mutations at the hot-spot remained unchanged. Unexpectedly, both Δdcm and Δvsr strains showed a two-fold increase in stationary-phase reversion frequency with respect to the wild-type strain. This result differed from an earlier finding where simultaneous deletion of both genes had no effect. We conclude that the adaptive mutation hot-spot is not caused by very-short-patch mismatch repair. Instead, our data suggest that dcm and vsr independently influence adaptive mutagenesis rate, possibly through previously unrecognized ‘moonlighting’ functions. Future work will aim to uncover the mechanism behind this unique adaptive mutational spectrum, advancing our understanding of stress-induced mutagenesis. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025.