Vertical yellow lines represent the positions of polymorphic sites, the green line LY2157299 in vitro depicts the position of the point mutation that is responsible for Rif resistance in J99-R3. Numbers below the panel: position relative to the Rif resistance point mutation, negative values indicate upstream nucleotides. The rows between 26695 and J99-R3 depict 30 sequences randomly selected from 92 clones
sequenced for the wt, and all 28 uvrC clones analyzed for import length. Any fragment surrounded by two sites identical to the donor is shown in red, any fragment surrounded by two sites identical to the recipient is shown in blue, and the remainder of the sequence is in white. Consequently, each sequence is shown as a mosaic of colors, where blue indicates DNA from the recipient, red DNA from the donor, and white DNA of unresolved origin. There was no significant change of the import length in the uvrA, uvrB, and ΔuvrD mutants. Strikingly, the inactivation of uvrC had a strong and highly significant effect on the length of imports of donor DNA into the recipient H. pylori genome (Figure 3;
Table 1). Indeed, the MLE of the imports increased more than 2-fold in the uvrC mutant compared to the wild type strain 26695 (3766 bp vs. 1681 bp, respectively). A functional complementation of this mutant restored this phenotype to wild type values, confirming that the generation of long imports was due to the absence of uvrC. None of Vismodegib mw Glutamate dehydrogenase the four mutants showed a significant change in the frequency of ISR (Table 1). Table 1 Maximum likelihood estimation (MLE) of the mean length of donor DNA imports in the rpoB gene and number of clones with ISR after natural transformation of H. pylori 26695 wild type strain and isogenic NER-deficient mutants Length of import
Isolates with ISR Dataset Isolates MLE (bp) BF Number BF 26695 wt 95 1681 9 uvrA 26 2451 0.31 0 0.35 uvrB 24 2887 1.22 2 0.15 uvrC 28 3766 49.04 1 0.17 uvrC comp 35 1781 0.12 7 0.78 Δ uvrD 38 2155 0.16 6 0.33 Very strongly significant results (Bayes Factor (BF) >30) are marked in bold. Discussion The nucleotide excision repair (NER) is a mechanism by which DNA lesions causing distortions of the helical structure (“bulky lesions”, induced by a variety of chemical agents and ultraviolet light) can be repaired. In E. coli, NER also acts on non-bulky lesions such as oxidized or methylated bases, suggesting overlapping activities of the BER and NER systems for some substrates [27, 28]. The H. pylori genome contains orthologs of all four NER genes, uvrA-D (Additional file 3: Figure S3), however the function of most of these genes, and their involvement in the unusual genetic variability of this pathogen were poorly characterized. Our data show that inactivation of each of the four H. pylori NER genes strongly increased UV sensitivity, confirming that they are indeed functional homologs of the E. coli NER genes [29, 30]. Mutation rates Inactivation of H.