PKD1 unusual DNA conformations are recognized by nucleotide excision repair

The 2.5-kilobase pair poly(purine pyrimidine) (poly(R.Y)) tract present in intron 21 of the polycystic kidney disease 1 (PKD1) gene has been proposed to contribute to the high mutation frequency of the gene. To evaluate this hypothesis, we investigated the growth rates of II Escherichia coli strains , with mutations in the nucleotide excision repair, SOS, and topoisomerase I and/or gyrase genes, harboring plasmids containing the full-length tract, six 5'-truncations of the tract, and a control plasmid (pSPL3), The full-l ength poly(R.Y) tract induced dramatic losses of cell viability during the first few hours of growth and lengthened the doubling times of the populati ons in strains with an inducible SOS response. The extent of cell loss was correlated with the length of the poly(R.Y) tract and the levels of negativ e supercoiling as modulated by the genotype of the strains or drugs that sp ecifically inhibited DNA gyrase or bound to DNA directly, thereby affecting conformations at specific loci. We conclude that the unusual DNA conformat ions formed by the PKD1 poly(R.Y) tract under the influence of negative sup ercoiling induced the SOS response pathway, and they were recognized as les ions by the nucleotide excision repair system and were cleaved, causing del ays in cell division and loss of the plasmid, These data support a role for this sequence in the mutation of the PKD1 gene by stimulating repair and/o r recombination functions.