Mutability and importance of a hypermutable cell subpopulation that produces stress-induced mutants in Escherichia coli.

Ivan Matic,Caleb Gonzalez,Lilach Hadany,Susan M Rosenberg,Mellanie Price,P J Hastings,Rebecca G Ponder

doi:10.1371/journal.pgen.1000208

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https://doi.org/10.1371/journal.pgen.1000208

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Abstract

In bacterial, yeast, and human cells, stress-induced mutation mechanisms are induced in growth-limiting environments and produce non-adaptive and adaptive mutations. These mechanisms may accelerate evolution specifically when cells are maladapted to their environments, i.e., when they are are stressed. One mechanism of stress-induced mutagenesis in Escherichia coli occurs by error-prone DNA double-strand break (DSB) repair. This mechanism was linked previously to a differentiated subpopulation of cells with a transiently elevated mutation rate, a hypermutable cell subpopulation (HMS). The HMS could be important, producing essentially all stress-induced mutants. Alternatively, the HMS was proposed to produce only a minority of stress-induced mutants, i.e., it was proposed to be peripheral. We characterize three aspects of the HMS. First, using improved mutation-detection methods, we estimate the number of mutations per genome of HMS-derived cells and find that it is compatible with fitness after the HMS state. This implies that these mutants are not necessarily an evolutionary dead end, and could contribute to adaptive evolution. Second, we show that stress-induced Lac+ mutants, with and without evidence of descent from the HMS, have similar Lac+ mutation sequences. This provides evidence that HMS-descended and most stress-induced mutants form via a common mechanism. Third, mutation-stimulating DSBs introduced via I-SceI endonuclease in vivo do not promote Lac+ mutation independently of the HMS. This and the previous finding support the hypothesis that the HMS underlies most stress-induced mutants, not just a minority of them, i.e., it is important. We consider a model in which HMS differentiation is controlled by stress responses. Differentiation of an HMS potentially limits the risks of mutagenesis in cell clones.

Highlights

Stress-induced mutational processes are responses to growthlimiting environments whereby mutations are produced at an accelerated rate, some of which may confer a growth advantage
As seen previously [19], we found that a strain carrying both a regulatable chromosomal expression cassette of the I-SceI enzyme and its cutsite on the F’ plasmid near lac showed a 70-fold increase in Lac+ mutation rate (Figure 3A,D) above that promoted by TraIdependent DNA breaks at the transfer origin of the F’ in the ‘‘wildtype’’ control cell
The unique sequence spectrum of the majority of stress-induced Lac+ reversion mutations was observed in those Lac+ mutants demonstrably descended from the hypermutable cell subpopulation (HMS): those carrying phenotypically-detectable secondary mutations in their genomes (Figure 1), implying that HMS-descended and most stress-induced Lac+ reversions form via the same mechanism

Summary

Introduction

Stress-induced mutational processes are responses to growthlimiting environments whereby mutations are produced at an accelerated rate, some of which may confer a growth advantage. The study of stress-induced-mutagenesis mechanisms is expanding our understanding of genome instability and cellular and organismal adaptability to environmental challenges (reviewed [1,2]). Stress-induced mutagenesis may potentially accelerate evolution when cells/organisms are maladapted to their environments, i.e., when they are stressed. Stressinduced mutagenesis mechanisms appear to be widespread and important in nature. Stressinduced mutagenesis mechanisms present appealing models for mutagenesis underlying evolution of antibiotic resistance, evasion of the immune response by pathogens, aging, and for genomic instability underlying tumor progression and resistance to chemotherapeutic drugs, all of which are fueled by mutations and occur in stress-provoking environments (reviewed by [2,7])

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