Fragmentation of replicating chromosomes triggered by uracil in DNA

The dut mutants of Escherichia coli fail to hydrolyze dUTP and thus incorporate uracil into their DNA, suffering from chromosomal fragmentation. The postulated mechanism for the double-strand DNA breaks is clustered uracil excision, which requires high density of DNA-uracils. However, we did not find enough uracil residues or excision nicks in the DNA of dut mutants to account for clustered uracil excision. Using a dut recBC(Ts) mutant of E. coli to inquire into the mechanism of uracil-triggered chromosomal fragmentation, we show that this fragmentation requires DNA replication and, in turn, inhibits replication of the chromosomal terminus. As a result, origin-containing sub-chromosomal fragments accumulate in dut recBC conditions, indicating preferential demise of replication bubbles. We propose that the basic mechanism of the uracil-triggered chromosomal fragmentation is replication fork collapse at uracil-excision nicks. Possible explanations for the low level terminus fragmentation are also considered.