Intragenic Domains of Strand-specific Repair inEscherichia coli

Abstract

Heterogeneity of DNA repair has been observed at different levels of genomic organization, including chromatin domains, expressed genes and DNA strands. If heterogeneity also existed intragenically, it could reveal fine details of the excision repair mechanismin vivo.Here we measure the frequency of UV-induced cyclobutane pyrimidine dimers at individual nucleotides within defined portions of twoEscherichia coligenes,laclandlacZ, at various times after irradiation. Two domains of differential repair rates were apparent, with repair being slow at nucleotides adjacent to the transcription start sites. InlacZ, the domain of faster repair began 32 bases downstream of the transcription start site and required themfdgene. Sincemfdcodes for a transcription-repair coupling factor, this transcription-coupled repair system evidently becomes operative downstream of the initiation complex regionin vivo.Unexpectedly, however, (1) anmfdmutation reduced repair in the downstream domain even when transcription was at a very low level and (2) induction oflacZtranscription with isopropyl-β-d-thiogalactoside overcame this reduction. Evidently, the Mfd transcription-repair coupling factor is required for basal levels of strand-specific repair in this gene, but induced levels of repair are related to transcription through another mechanism.