Selective Inbreeding: Genetic Crosses Drive Apparent Adaptive Mutation in the Cairns-Foster System ofEscherichia coli

Abstract

The Escherichia coli system of Cairns and Foster employs a lac frameshift mutation that reverts rarely (10−9/cell/division) during unrestricted growth. However, when 108 cells are plated on lactose medium, the nongrowing lawn produces ∼50 Lac+ revertant colonies that accumulate linearly with time over 5 days. Revertants carry very few associated mutations. This behavior has been attributed to an evolved mechanism (“adaptive mutation” or “stress-induced mutagenesis”) that responds to starvation by preferentially creating mutations that improve growth. We describe an alternative model, “selective inbreeding,” in which natural selection acts during intercellular transfer of the plasmid that carries the mutant lac allele and the dinB gene for an error-prone polymerase. Revertant genome sequences show that the plasmid is more intensely mutagenized than the chromosome. Revertants vary widely in their number of plasmid and chromosomal mutations. Plasmid mutations are distributed evenly, but chromosomal mutations are focused near the replication origin. Rare, heavily mutagenized, revertants have acquired a plasmid tra mutation that eliminates conjugation ability. These findings support the new model, in which revertants are initiated by rare pre-existing cells (105) with many copies of the F’lac plasmid. These cells divide under selection, producing daughters that mate. Recombination between donor and recipient plasmids initiates rolling-circle plasmid over-replication, causing a mutagenic elevation of DinB level. A lac+ reversion event starts chromosome replication and mutagenesis by accumulated DinB. After reversion, plasmid transfer moves the revertant lac+ allele into an unmutagenized cell, and away from associated mutations. Thus, natural selection explains why mutagenesis appears stress-induced and directed.

Beyond horizontal gene transfer: the role of plasmids in bacterial evolution

“…This mutagenesis, which seems to be restricted to plasmid genomes, occurs through an increase in PCN in a subpopulation of cells. Conjugative transfer of these plasmids between clone mates further amplifies plasmid genomes, which are then subject to extensive mutagenesis mediated by the plasmid-encoded, error-prone polymerase DinB 47,112 .…”

SUMO and cellular adaptive mechanisms

“…Most studies of directed adaptive mutation, which remains a highly controversial concept (for example, see ref. 18 ), have been performed in Escherichia coli , but additional studies have been reported in other bacteria and eukaryotes, including yeast and mammals 17 , 19 , 20 . While there is no consensus regarding whether directed mutation can occur, there is a range of reported evidence for stress-induced hypermutation, which can increase the probability of creating favorable mutations that can be acted upon by natural selection 21 .…”

Plasmids modulate microindel mutations inAcinetobacter baylyiADP1

“…This is well illustrated by the plasmid-mediated spread of genes responsible for antimicrobial resistance, virulence factors and the ability to degrade xenobiotics (Heuer & Smalla, 2012). Other plasmid accessory genes may promote bacterial adaptation by enhancing mutagenesis instead, an effect that has been linked to plasmid-encoded error-prone polymerases (Woodgate & Sedgwick, 1992; Remigi et al, 2014; Sano et al, 2014; Nguyen et al, 2020). Although plasmids confer new phenotypes directly associated to the accessory genes they encode, they may also collaterally manipulate host behaviour via regulatory cross-talks, which result in the indirect expression of further phenotypic variation (Billane et al, 2021) [e.g., altered host metabolism (Hall et al, 2024)].…”