Fig. 2.

MarA binding upstream of xseA is important for DNA repair in the presence of ciprofloxacin. a ChIP-seq data for MarA and σ⁷⁰ binding to the xseA locus. Data have been smoothed in a 100 bp window. b DNA sequence upstream of xseA (start codon in blue) is shown. Relevant DNA elements are labelled and arrows indicate orientation. The xseA transcription start (+1) was identified by Davies and Drabble³³. The 5′ end of the xseA1 and xseA2 DNA fragments are indicated by inverted black triangles. The xseA2 fragment carries the −36C mutation. c Electrophoretic mobility shift assays with the xseA1 fragment (+marbox) and the xseA2 fragment (−marbox). MarA was at a concentration of 0.3, 1.0 and 1.7 μM. d DNAseI footprinting experiment, using the xseA1 fragment, calibrated with a Maxam–Gilbert GA sequencing ladder. Positions relative to the xseA transcription start site (+1) are labelled. Concentrations of MarA are 0.3, 1.0, 1.7, 2.4 and 3.3 μM. The marbox is indicated by a green line. e Result of a β-galactosidase assay using lysates of JCB387 cells transformed with a reporter plasmid where lacZ expression is controlled by either xseA1 (+marbox) or xseA2 (−marbox). Error bars show standard deviation (n = 3). f The graph shows OD₆₅₀ values obtained for cultures of strain BW25113 xseA::kan grown in the presence or absence of 0.005 μg/ml ciprofloxacin. The BW25113 xseA::kan cells were transformed with pBR322 derivatives encoding xseA under the control of either the xseA1 fragment (+marbox) or the xseA2 fragment (−marbox). Error bars show standard deviation (n = 3). g Hoechst-stained BW25113 cells or the xseA::kan derivative. The term ‘complement’ denotes BW25113 xseA::kan transformed with pBR322 encoding xseA under control of the xseA1 fragment (+marbox) or the xseA2 fragment (−marbox). The scale bar is 5 μm and all panels are the same scale. h A pulse field gel electrophoresis experiment to analyse chromosomal integrity of BW25113 (WT) or the xseA::kan derivative (Δ). The xseA::kan derivative of BW25113 was transformed with either empty pBR322 (Δ¹), pBR322 encoding xseA under the control of xseA1 fragment (Δ²) or xseA2 (Δ³)