What is mutation? A chapter in the series: How microbes "jeopardize" the modern synthesis

Abstract

Mutations drive evolution and were assumed to occur by chance: constantly, gradually, roughly uniformly in genomes, and without regard to environmental inputs, but this view is being revised by discoveries of molecular mechanisms of mutation in bacteria, now translated across the tree of life. These mechanisms reveal a picture of highly regulated mutagenesis, up-regulated temporally by stress responses and activated when cells/organisms are maladapted to their environments-when stressed-potentially accelerating adaptation. Mutation is also nonrandom in genomic space, with multiple simultaneous mutations falling in local clusters, which may allow concerted evolution-the multiple changes needed to adapt protein functions and protein machines encoded by linked genes. Molecular mechanisms of stress-inducible mutation change ideas about evolution and suggest different ways to model and address cancer development, infectious disease, and evolution generally.

Fig 1. E. coli MBR models.

(a–c) RecBCD nuclease loads RecA HR protein onto ssDNA, similarly to human BRCA2 loading RAD51; basepairing with a strand of identical duplex DNA (gray, e.g., a sister chromosome). Parallel lines, basepaired DNA strands. Repair synthesis (dashed lines) is switched to a mutagenic mode by the general stress response (sigma S). DNA polymerase errors (d, purple X) generate indels (e, purple XX) and base substitutions (f, purple XX). Microhomologous MBR requires DNA Pol I for template switching to regions containing microhomology (g), of as little as a few basepairs, and initiates replication, creating genome rearrangements; (h) a duplicated chromosome segment (blue arrows) is shown here. Circled numbers and shading indicate the three main events in HR-MBR: ① a DSB and its repair by HR, ② the SOS response (pink), and ③ the general stress response (blue). Note that HR-MBR (d–f, purple) requires both the SOS response (②, pink, which up-regulates error-prone DNA Pol IV, necessary for HR-MBR) and general stress response (③, blue), but microhomologous MBR (g–h, blue) requires the general stress response but not SOS (③, blue). Figure modified from [12]. HR, homologous recombination; MBR, mutagenic break repair; ssDNA, single-stranded DNA.