Palindromes as substrates for multiple pathways of recombination in Escherichia coli

A 246-bp imperfect palindrome has the potential to form hairpin structures in single-stranded DNA during replication. Genetic evidence suggests that t hese structures are converted to double-strand breaks by the SbcCD nuclease and that the double-strand breaks are repaired by recombination. We invest igated the role of a range of recombination mutations on the viability of c ells containing this palindrome. The palindrome was introduced into the Esc herichia coli chromosome by phage lambda lysogenization. This was done in b oth wt and sbcC backgrounds. Repair of the SbcCD-induced double-strand brea ks requires a large number of proteins, including the components of both th e RecB and RecF pathways. Repair does not involve PI PriA-dependent replica tion fork restart, which suggests that the double-strand break occurs after the replication fork has passed the palindrome. In the absence of SbcCD, r ecombination still occurs, probably using a gap substrate. This process is also PriA independent, suggesting that there is no collapse of the replicat ion fork. In the absence of RecA, the RecQ helicase is required for palindr ome viability in a sbcC mutant, suggesting that a helicase-dependent pathwa y exists to allow replicative bypass of secondary structures.