Stationary phase deletions in Escherichia coli. I--Evidence for a new deletion pathway

Deletions in the plasmid pMC874 join the promoter of the km(r) (kanamycin resistance) gene coding for the enzyme aminoglycoside 3'-phosphotransferase to a promoterless lac operon downstream giving a phenotypic change from Lac(-)-->Lac(+). They differ from most deletions studied in Escherichia coli, which occur in actively dividing cells, in several important respects, as follows. (1) They occur in "resting" cells incubating on McConkey's or minimal lactose agar and increase in number gradually over a period of 1-2 weeks. Thus, like "adaptive" mutations, they are time rather than generation dependent. (2) They are extremely rare events (frequency 1x10(-11)-5x10(-11)) in wild type cells, but their frequency is increased between 1 and 2 orders of magnitude by null recC(-) mutations. In these respects they differ from "adaptive" mutations which are equally frequent in recC(+) and recC(-) cells. (3) Their frequency is not increased by mutations which stimulate log phase deletions. (4) Based on a computer search for homologies and sequencing of one deletion, it appears that they differ from log phase deletions in that they can occur in the absence of major terminal homologies (direct repeats) or intervening homologies (inverted repeats) which could stabilize a transient secondary structure and determine the deletion endpoints. Thus, they are not explained by the misaligned mutagenesis model. In conclusion, resting phase deletions occur through a totally different pathway from deletions in actively dividing cells and probably originate from unrepaired double strand breaks.