0; Bio-Rad). #HTS assay randurls[1|1|,|CHEM1|]# The 16S rRNA primers were used for normalization [29]. Crystal violet biofilm assay The assay was adapted from Nakao et al.[30] with the following modifications: E. coli were grown in LB broth for 16 h at 37°C and diluted to 5 × 106 CFU/mL in fresh LB broth with or without IPTG. Aliquots (800 μL) dispensed into polystyrene tubes (Falcon

352058, BD Biosciences) and incubated for 24 h at 37°C without shaking. Each data point represents the mean ± standard deviation of ten independent cultures. β-galactosidase activity assays The β-galactosidase activity from whole cells of KSK003 (λrpoS’-‘lacZ), KSK004 [SG30013 (λRpoS750::LacZ)] [31], RS8872 (λpnp’-‘lacZ in rnc+) [32], or RS8942 (λpnp’-‘lacZ in rnc14) [32] overexpressing YmdB from ASKA-ymdB (−) was determined as described by Miller [33]. The results are expressed as the means of three independent experiments. Protein gel electrophoresis

find more and Western blot analysis Overexpression of the YmdB and RpoS proteins was detected on Coomassie blue-stained 12% Mini-PROTEAN TGX Precast gels (Bio-Rad). Western blots for RNase III, YmdB, RpoS, or 6x Histidine-tagged YmdB were prepared as described [18], probed with antibodies (1:2,500 dilution) against YmdB, RNase III [18], RpoS (1RS1: Santa Cruz Biotechnology), or 6x Histidine-tagged YmdB (6xHis Epitope Tag Antibody: Thermo Scientific) and developed with Clarity™ western ECL substrate (Bio-Rad). To normalize the signals, antibodies against S1 protein [34] was used as a reference probe (1:100,000 dilution). Anti-rabbit IgG:HRP or anti-mouse IgG:HRP conjugates (Promega; 1:5000 dilution)

were used for YmdB/RNase III/S1 proteins or RpoS/6xHistidine tagged YmdB, respectively. Specific proteins were imaged using MyECL and quantified with myImage Analysis software (Thermo Scientific). Results Analysis of the E. coli transcriptome under conditions mimicking those of an RNase III mutant To identify which pathways and related genes are mediated by YmdB-modulated C-X-C chemokine receptor type 7 (CXCR-7) RNase III inhibition, a genome-wide analysis of mRNA abundance at single gene resolution was performed. In these experiments, total steady-state RNA extracted from IPTG-induced exponentially grown cells expressing either ASKA-ymdB (a part of the ASKA (−) library: a complete set of cloned individual E. coli genes encoding proteins with 6x histidines at the N-terminal end and no GFP fusion at the C-terminal end [35]); or pCA24N (a control vector without GFP at the C-terminal end) [29] were analyzed on customized ORF microarray chips. Duplicate arrays were performed with biological replicates to minimize experimental artifacts, and the gene expression profiles of 4,289 genes were averaged and analyzed. YmdB overexpression modulated the relative abundance of more than 2,000 transcripts (data not shown). Of these, 129 genes were strongly regulated (changes in expression of either >1.5 or <0.6 fold) (Additional file 1: Table S3).