MOESM2 of Revisiting the in vivo GlnR-binding sites at the genome scale in Bacillus subtilis

Additional file 2: Table S1. Mapping of GlnR DNA binding sites by ChIP-on-chip. ChIP-on-chip experiments were performed and data were analysed as previously described [32] using the method described by Reppas et al. [34]. GlnR was purified in two biological replicates for each condition of growth. This table lists all significantly enriched DNA regions by ChIP-on-chip experiment performed with a GlnRSPA expressing Bacillus subtilis strain

Additional file 2: Figure S2. of The MarR-like protein PchR (YvmB) regulates expression of genes involved in pulcherriminic acid biosynthesis and in the initiation of sporulation in Bacillus subtilis

Effect of iron starvation on the expression of cypX and yvmB. The BFA815 (cypX::lacZ) and BSAS108 (pyvmB’-lacZ) strains were cultivated in LB medium until OD600 of 1. Samples of 2 ml of the cultures were spread onto solid LB medium containing 20 μg.ml−1 X-gal. A drop of 10 μl 10 mM bipyridyl was deposited at the center of each plate. Blue rings corresponded to expression of the fusion in cells around the inhibition zone of bipyridyl drops. (PDF 75 kb

Count table from RNAseq data.

(XLSX)</p

List of discriminatory genes in components 1 and 2 with PLS-DA analysis.

The tool eggNOG-mapper was used for functional annotation based on precomputed orthology assignments. (XLSX)</p

Exploratory analyses of each dataset.

After processing the raw data, we checked the distribution of raw counts and performed principal component analysis. (TIF)</p

Sample clustering.

The quality of the expression matrix was evaluated by sample clustering based on the distance between different samples, measured as Spearman’s correlation. No outliers were detected. (TIF)</p

Flow chart of data preparation, processing, and analysis.

(TIF)</p

List of the genes in the detected modules.

(XLSX)</p

Rho inactivation increases expression of KinA and KinB kinases.

<p>WT (W) and RM (r) cells containing <i>kinA</i>-SPA or <i>kinB</i>-SPA translational fusions at natural chromosomal loci were grown in LB (lanes 1–4) or sporulation-inducing DS medium (lanes 5–10) to mid-exponential (expo; OD₆₀₀ ∼ 0.5) or stationary (stat; OD₆₀₀∼ 1.5) phases and analyzed for KinA and KinB proteins using ANTI-FLAG M2 monoclonal antibodies. Equal amounts of protein were loaded onto the gel as quantified by the Bradford assay. To control equilibrium between the samples, total protein extracts from cells with <i>kinB</i>-SPA fusion were analyzed for MreB protein using anti-MreB specific antibodies.</p

Impact of Rho inactivation on swarming motility of <i>B</i>. <i>subtilis</i> cells.

<p>(A) Motility defect of the NCIB 3610 RM cells can be partially suppressed by the deletion of <i>slrR</i> and ectopic expression of <i>flhO-flhP</i> genes. Bacterial cultures were grown to an OD₆₀₀ 0.5, concentrated and spotted on the plate as described (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006909#sec019" target="_blank">Materials and methods</a>). The images were acquired after 20 hours of incubation at 37°C. Each icon represents top-grown image of centrally inoculated Petri plate (diameter 9 cm) containing LB and 0.7% of agar. Relevant genotypes are indicated on the side of each image. The repaired back to the wild type NCIB 3610 RM is denoted as <i>rho</i> wt*. The experiment was reproduced at least five times and included three biological replicas for each strain. The results from the representative experiment are presented. (B) Quantitative swarming assay of the indicated NCIB 3610 (blue lines) and isogenic NCIB 3610 RM (red lines) derivative strains. Values represent the mean of at least five experiments. (C) Impact of <i>rho</i> deletion on sense and antisense transcription of the <i>flhO-flhP</i> operon in the <i>B</i>. <i>subtilis</i> 1012 cells. Expression profiles are from the <i>B</i>. <i>subtilis</i> expression data browser (<a href="http://genome.jouy.inra.fr/cgi-bin/seb/index.py" target="_blank">http://genome.jouy.inra.fr/cgi-bin/seb/index.py</a>). Vertical bar on the top line indicates position of predicted putative terminator (shown in D). Sections show annotated genome (top) and expression profiles on the (+) and (–) strands (mid and bottom sections). Wild type (black) and RM (red) profiles are shown. (D) MFOLD [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006909#pgen.1006909.ref083" target="_blank">83</a>] predicted secondary structure (ΔG = −16, 30) within <i>flhP</i> asRNA.</p