Deletion of the <i>dps</i> gene affects <i>rpoA</i> and <i>rpoB</i> expression.

<p><b>A:</b> Profiles of the Dps binding sites obtained in two experiments (indicated) for the genomic region with three operons of ribosomal genes (running window of nine 35 bp bins). Genes are represented by blue horizontal arrows; magenta lines show ribosomal operons. Vertical arrows mark locations of inverted repeats (if longer than 7 bp). <b>B:</b> Band shift assays performed for indicated genomic loci. The regulatory region of the <i>dps</i> gene was used as a positive control for all band shift assays in this study. Fragment from the <i>lacZ</i> coding sequence was used as a reference gene for qRT-PCR experiments. Positioning of primers for amplification (<b>F</b> and <b>R</b>) is indicated in panel <b>A</b> of this figure, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.g006" target="_blank">Fig 6A</a> (for the <i>dps</i> regulatory region) and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.s003" target="_blank">S3 Fig</a> (for <i>rpoA</i> and <i>lacZ</i>). <b>C:</b> Changes in the expression efficiency of selected genes in response to <i>dps</i> deletion. Primers used for reverse transcription and consecutive PCR are designated as RT and PCR, respectively, here and all other figures. Expression levels were estimated based on 3 and 5 biological samples (3–18 technical repeats in each) for <i>rpoA</i> and <i>rpoD</i>, respectively. Error bars show an average deviation. Statistical significance was assessed using Student’s t-test.</p

Large-scale profiles of the Dps targets correlate with the landscape of direct and inverted repeats and the pattern of Fis binding sites.

<p><b>A:</b> Distribution of the Dps contact regions along the <i>E</i>. <i>coli</i> MG1655 genome identified by CLC GW in two experiments (the default settings). The areas covered by Dps are combined in 100,000 bp bins and plotted as percentage to the total length of all sites occupied by Dps. <b>B</b>: The same for the contact sites of Fis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.ref049" target="_blank">49</a>], IHF [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.ref051" target="_blank">51</a>], H-NS [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.ref049" target="_blank">49</a>] and RNAP [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.ref050" target="_blank">50</a>] from the cells grown in conditions similar to those used in our experiments. The plot for Dps shows the distribution of the sites from the combined set (<b>CS</b>) (Page 3, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.s009" target="_blank">S3 Table</a>). <b>C:</b> The same for direct (5–24 bp separated by 1–15 bp) and inverted (5–18 bp separated by 3–20 bp) repeats collected from the genome of <i>E</i>. <i>coli</i> MG1655 using Unipro UGENE [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.ref053" target="_blank">53</a>].</p

Dps shares its binding sites with other proteins of bacterial nucleoid and has affinity to REP-elements and <i>promoter islands</i>.

<p>Intersection of Dps targets (<b>A</b>) and sites unbound by Dps (<b>B</b>) with structural and functional elements of bacterial genome was estimated as described above for repeated sequences and plotted as fold ratio to the expected values. Bent black arrows on the bottom schematically show areas occupied by CS or UR. Gray rectangles and numerals inside indicate the expected number of common base pairs if compared modules are independently distributed along the genome. Gray and colored bent arrows show registered overlap calculated in 1 bp resolution. Numerals in parenthesis indicate the size of compared sets. Genomic locations of REP elements were taken from KEGG DataBase (<a href="http://www.genome.jp/kegg/" target="_blank">http://www.genome.jp/kegg/</a>, [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.ref063" target="_blank">63</a>]), and fold ratios obtained for 302 REP-sequences containing 1–3 REP-modules (14–100 bp) were plotted. Analyzed ChIP-chip and ChIP-seq data sets were obtained from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.ref046" target="_blank">46</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.ref051" target="_blank">51</a>] for cells grown in LB medium (LB), M9 medium with fructose (M9) or MOPS minimal medium with glucose (GMM), harvested at early (EE), middle (ME) or late (LE) exponential phase or upon transition to the steady growth (TS).</p

Dps-binding sites are enriched with inverted repeats.

<p>The overlap between sequences of CS (colored box-plots) and UR (gray boxes) with direct or inverted repeats was characterized by the parameter <b>K</b>_<b>ij</b> as described in the text. Black dot on the right panel shows one outlier. Box-plots with statistically significant differences are provided with corresponding p-values. Regions of bound and unbound sets overlapping with repeated sequences of both types are indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182800#pone.0182800.s009" target="_blank">S3 Table</a>.</p