chi*, a chi-related 11-mer sequence partially active in an E-coli recC* strain

Background: chi sequence (5'GCTGGTGG) of Escherichia coli was first identified as a site that increased the plaque size of bacteriophage lambda. Subsequent studies showed that this site is responsible for both the attenuation of RecBCD exonuclease activity and the promotion of RecA, RecBCD-mediated recombination. It is known that bacteriophage lambda containing the chi site makes very small plaques on a recC(*) (recC1004) mutant because chi is not recognized by the RecBC(*)D mutant enzyme. Results: We cloned E. coli chromosomal fragments in chi which allowed chi to form larger plaques on this recC(*) mutant. The fragments were found to share a chi-like 11-mer sequence, 5'GCTGGTGCTCG. Substitution of these fragments with a synthetic 11-mer of this sequence and single-base-pair substitution analysis of its last four nucleotides demonstrated that this sequence is both necessary and sufficient for the observed activity. The sequence, designated chi(*) (chi-star), protected rolling-circle DNA replication in the recC(*) mutant and in the recBCD(+) strain, most likely because it attenuated the exonuclease activity of the RecBC(*)D and RecBCD(+) enzyme. chi(*), did not significantly stimulate lambda recombination in two assays. Conclusion: We have discovered that a mutant RecBCD enzyme responds, in vivo, to a longer chi variant.