Clustering of ϰ Sequence in Escherichia coli Genome

Abstract

An 8-mer DNA sequence called ϰ (5′-GCTGGTGG) is present on the Escherichia coli chromosome at a high frequency. It is responsible for both the attenuation of RecBCD exonuclease activity and the promotion of RecABCD-mediated homologous recombination, ϰ was first identified as a site that increased plaque size of bacteriophage λ. λ containing ϰ makes very small plaques on a recC^* (recC1004) mutant because ϰ is poorly recognized by the RecBC^*D mutant enzyme. We cloned E. coli chromosomal fragments in λ that allowed λ to form larger plaques on this recC^* mutant as well as on the rec⁺ parent. One identified fragment contained a cluster of two copies of ϰ and several ϰ-like sequences with the same orientation. It increased recombination in the rec⁺ strain more than a fragment with one ϰ did. This fragment was within the rep gene, whose helicase product is known to be required for growth in the absence of functional RecBCD enzyme. The possibility that RecBCD enzyme might interact both with the rep gene and its product is discussed. Many of the other ϰ clusters identified in the E. coli genome database lie within genes for membrane proteins. The possible significance of these findings is discussed.