005% surfactant P20 (GE

Healthcare). C. diffcile LexA repressor (2.6 μM), interacting with either the 22 bp recA operator DNA fragment or with the 22 bp non-specific DNA fragment derived from the recA operator, was passed over the sensor chip with immobilized RecA* (~2000 response units). LexA specific DNA (recA operator) or non-specific DNA, with 6 nucleotide changed in comparison to the specific DNA, was prepared by hybridising primers (1:1 mol to mol ratio) 5′-CAAGAGAACAAATGTTTGTAGA-3′ and 5′-TCTACAAACATTTGTTCTCTTG-3′or 5′-CAAGACCGGAAATCCTTGTAGA-3′ and 5′-TCTACAAGGATTTCCGGTCTTG-3′, VX-680 nmr respectively. The RecA*-LexA interaction was assayed at 10 μl/min for 60 s and the dissociation followed for 60 s. The sensor chip was regenerated as described [25]. Repressor cleavage assay Activation of either E. coli or C. difficile RecA (10 μM) nucleoprotein filament was performed on ice for 2 h as described [34]. RecA*-stimulated (~2 μM) cleavage of LexA were performed in 20 mM Tris, pH 7.4, 5 mM MgCl2, 1 mM ATP-γ-S (Sigma), and 1 mM DTT as described [25]. Samples were resolved on 12% SDS PAGE gels in MOPS PD0332991 ic50 running buffer (Invitrogen) and stained by Page blue Selleckchem LDC000067 protein stain (Thermo Scientific). The resolved bands were quantified using a G:Box (Syngene). The integrated optical densities of

the LexA monomers were determined. The LexA levels throughout the time course were compared and are presented as the ratio of the density value for the sample at time indicated as Dipeptidyl peptidase 0 min relative to the density value obtained from the samples obtained later in the LexA cleavage reaction. The experiments were performed two times and representative gels are shown. Acknowledgments The research leading to these results has received funding from the European Community’s Seventh Framework Programme FP7/2007-2013 under grant agreement No. 237942. Part of this work was supported by grants from the Slovenian Research Agency (Z1-2142 and

J4-2111). Electronic supplementary material Additional file 1: Table S1: List of genomes used for analysis of SOS regulon and LexA variability. The names of the strains used for SOS regulon analysis are additionally bolded. (XLSX 15 KB) Additional file 2: Figure S1: Comassie stained C. difficile (CD) LexA and RecA proteins and the LexA protein from Escherichia coli (EC). Proteins used in the study were more than 95% pure. Approximately 5 μg of each protein was loaded on the SDS-PAGE gel. (TIFF 2 MB) Additional file 3: Table S2: Pairs of primers used to construct double stranded DNAs harbouring predicted LexA target sites. Putative LexA operators are underlined. (XLSX 12 KB) References 1. Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC: Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli . Genetics 2001, 158:41–64.PubMedCentralPubMed 2. Erill I, Campoy S, Barbe J: Aeons of distress: an evolutionary perspective on the bacterial SOS response.