Deletions at stalled replication forks occur by two different pathways

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Abstract
Replication blockage induces non‐homologous deletions in Escherichia coli. The mechanism of the formation of these deletions was investigated. A pBR322–mini‐oriC hybrid plasmid carrying two E.coli replication terminators (Ter sites) in opposite orientations was used. Deletions which remove at least the pBR322 blocking site (named Ter1) occurred at a frequency of 2×10−6 per generation. They fall into two equally large classes: deletions that join sequences with no homology, and others that join sequences of 3–10 bp of homology. Some 95% of the deletions in the former class resulted from the fusion of sequences immediately preceding the two Ter sites, indicating a direct role for blocked replication forks in their formation. These deletions were not found in a topA10 mutant, suggesting a topoisomerase I‐mediated process. In contrast, deletions joining short homologous sequences were not affected by the topA10 mutation. However, the incidence of this second class of deletions increased 10‐fold in a recD mutant, devoid of exonuclease V activity. This indicates that linear molecules are intermediates in their formation. In addition, ∼50% of these deletions were clustered in the region flanking the Ter1 site. We propose that they are produced by repair of molecules broken at the blocked replication forks.