Average Coefficients of Gene–Drug Interactions

<div><p>The <i>β<b>₅</b>, β<b>₆</b>,</i> and <i>β<b>₇</b></i> values in different functional groups (A) and association between the <i>recA</i> and <i>topA</i> mutation effects (B) are shown.</p><p>(A) For the sake of convenience, the average coefficients are shown with opposite signs (−β<i>₅</i><i>,</i> −β<i>₆</i>, and −β<i>₇</i>), so that the positive values indicate the increase in transcript levels and the negative indicates the decrease. The number of genes in each functional group is in parenthesis, and the error bars represent two standard errors.</p><p>(B) The interactions between the <i>recA–</i>drug <i>(−β₅</i>) and <i>topA–</i>drug <i>(−β₆</i>) effects can be seen as the positive correlations for 36 selected genes <i>(r</i> = 0.82; <i>p</i> < 0.1 in both −β<i>₅</i> and −β<i>₆</i>).</p></div

Effect of RecA on the Topo I-Catalyzed Relaxation Reaction

<div><p>(A) DNA relaxation reaction catalyzed by Topo I in the presence of RecA. The substrate (lanes 1 and 7), cccDNA of pBR322, was incubated with increasing amounts of Topo I in the absence (lanes: 2–6) or presence of 5,600 ng (3 nt per RecA monomer) of RecA (lanes: 8–11) at 37 °C for 30 min and resolved on the vertical agarose gel as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020152#s4" target="_blank">Materials and Methods</a>.</p><p>(B) ATP-dependence of the RecA effect. The substrate plasmid DNA (lane: 1) was incubated with 0.1 pmol of Topo I and the indicated amounts of RecA in the absence (lanes: 2–5) or presence of ATP (lanes: 6–9).</p></div

Spatial Correlations of Temporal Transcriptional Profiles Elicited by Gyrase Inhibition

<p>Temporal transcriptional profiles observed in the wild-type (A) and isogenic mutant strains (B). Pair-wise correlations of temporal transcript profiles of 4,000 genes, arranged in the chromosomal order, are shown on a colorimetric scale for the whole chromosome (A) and the <i>oriC</i> proximal region (B). For spatial correlations around the <i>n</i>-th gene (<i>n</i> on the <i>x</i>-axis) in the chromosomal order, each <i>y</i>-axis includes 20 Pearson correlations of temporal profile pairs, (<i>n</i> − 1, <i>n</i> + 1), (<i>n</i> − 2, <i>n</i> +2),...(<i>n</i> − 19, <i>n</i> + 19), and (<i>n</i> − 20, <i>n</i> + 20). Chromosomal regions with high correlations exhibit symmetric red (positive) or blue (negative) triangles. Differentially expressed genes were significantly enriched in the regions marked with horizontal bars. The regions in which at least 16 consecutive genes show significant high correlations are enumerated. The statistical significance is estimated by the comparison with 5,000 randomly sampled subsets of temporal profiles.</p

Comparison of the GC Content in Upstream and Coding Regions of Activated and Repressed Genes

<div><p>(A) The GC content of the DNA regions from −2,000 to +1,500 nt, relative to the translation start site, of 84 activated (red) and 95 repressed (blue) genes was calculated with a 100-nt moving window (black: the average GC content of the genome). The significance of the GC content differences in a given region was determined by comparing the average GC content of the repressed genes with the GC content of 10,000 randomly sampled sets of similar fragments in the genome.</p><p>(B) DNA windows, from 1 nt to 500 nt, were compared to assess their GC content in −500-nt upstream regions. The <i>p</i>-values were determined by comparing the averages of the maximal GC content values of the activated (red square), or repressed (blue triangle), genes with the corresponding values of 10,000 randomly sampled sets from the whole genome.</p></div

SOM Analysis of Temporal Transcriptional Profiles

<p>U-matrix (left side of panel) and weight vectors (right side of panel) of a self-organizing feature map of temporal transcriptional profiles observed after the addition of norfloxacin to the wild-type (A), <i>recA</i> (B), <i>topA</i> (C), or <i>dnaC</i>(Ts) (D) mutant. Transcript levels measured at 5, 10, 15, and 20 min of the treatment were compared with those of the non-treated cells (0 min; first time point) for 1,109 genes that showed differential expression in at least one strain. Each contoured hexagon (left side of panel) has a corresponding weight vector that represents temporal responses (0 to 20 min, right side of panel). Small hexagons indicate map units that are colored according to the medians of the surrounding hexagon with a contour line passing through.</p

Wild-type strains of , and were grown in MOPS glucose plus nicotinate or MOPS glucose defined-rich media

The data are from two independent experiments (open and closed symbols). Growth curves (, MOPS glucose medium; , MOPS rich medium) and Lrp protein levels (, glucose; , rich) are shown. Equal amounts of total protein were loaded in each lane, and a standard curve of purified Lrp was included on each gel for quantitation. shows a comparative western blot. Cell pellets were boiled and equal amounts of total protein from (Ec) and (Pm) were resolved side-by-side via SDS polyacrylamide gel electrophoresis. The subsequent blot was probed with polyclonal antiserum raised against Lrp.<p><b>Copyright information:</b></p><p>Taken from "Limited functional conservation of a global regulator among related bacterial genera: Lrp in , and "</p><p>http://www.biomedcentral.com/1471-2180/8/60</p><p>BMC Microbiology 2008;8():60-60.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2374795.</p><p></p

Limited functional conservation of a global regulator among related bacterial genera: Lrp in , and -7

Ng standard errors. At least four points from each of two independent experiments were used to generate each plotted value. Conditions were MOPS-glucose minimal medium, supplemented as described in Methods, in logarithmic (MinLog) or stationary phase (MinSta), or MOPS glucose defined rich medium in those growth phases (RchLog, RchSta). . Direct comparison of mRNA levels.. A baseline amount of total RNA (from a mid-log phase culture in MOPS glucose plus nicotinate) was mixed with varying amounts of test RNA (all from log-phase cultures) from glucose (open circle) or rich (closed circle) cultures. The mixes were used as template for simultaneous amplification with three primer pairs. If the test cDNA preparation has the same proportion of cDNA as the reference pool, the detected amount of cDNA should rise with a slope of 1.0 (actual . detected, based on the varied amounts of test cDNA added); this is shown as a dotted line in each panel.<p><b>Copyright information:</b></p><p>Taken from "Limited functional conservation of a global regulator among related bacterial genera: Lrp in , and "</p><p>http://www.biomedcentral.com/1471-2180/8/60</p><p>BMC Microbiology 2008;8():60-60.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2374795.</p><p></p

In every panel, the x-axis shows the gene expression ratio for 12 Δrelative to that in the same strain complemented by (pEcoLrp)

The y-axes indicate the equivalent ratio, where the complementation is by vector alone (pCC1) or the alleles from (pVchLrp) or (pPmiLrp). Full complementation relative to that by pEcoLrp would yield a slope of 1.0 for the linear fit. . This column shows responses of the gene set yielding statistically-significant increases in expression associated with mutation in , as reflected by an expression ratio significantly above 1.0 on the x-axis. This set includes genes that are repressed (directly or indirectly) by Lrp. . This column includes the set of genes showing significant decreases in expression associated with mutation in , indicating direct or indirect activation by Lrp. . This column shows the set of 57 genes recognized in RegulonDB [71, 72] as being directly controlled by Lrp, whether the control is positive or negative. This set includes genes that are controlled by Lrp, but not under the growth conditions used by us, so the cluster of genes showing little or no effect of Lrp is not surprising [66, 69]. The relative transcript abundances were estimated from at least three independent biological replicas using a linear model similar to one introduced before [141, 142]. Significantly expressed genes were identified at a fixed false discovery rate of 5% at the 90percentile [138]. Details of the statistical analysis of these data are in the text, and a list of the 57 RegulonDB Lrp targets is in the Methods section.<p><b>Copyright information:</b></p><p>Taken from "Limited functional conservation of a global regulator among related bacterial genera: Lrp in , and "</p><p>http://www.biomedcentral.com/1471-2180/8/60</p><p>BMC Microbiology 2008;8():60-60.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2374795.</p><p></p

Strains, all carrying 10 and Δ, were transformed with plasmids carrying various alleles (or vector control)

Transformants were grown in unsupplemented MOPS glucose medium. . Western blot analysis of Lrp accumulation (Eco, Lrp; Pmi, Lrp; Vch, Lrp; pCC1, vector control) using polyclonal antiserum raised against Lrp. The arrow indicates the direction of electrophoresis. . P(B), P(C) and P(D) activity were measured via ONPG hydrolysis, and plotted . culture density to ensure that the cultures were in balanced growth. The Lrp orthologs used are from (triangles) and (squares), as well as the positive control (circles) and the vector control (diamonds). . Isoleucine, Leucine and Valine was added to the medium ("+Leu") for experiments depicted in the lower panels: (E), (F) and (G). The correlation coefficients for the least-squares fits to the data were all at least 0.97.<p><b>Copyright information:</b></p><p>Taken from "Limited functional conservation of a global regulator among related bacterial genera: Lrp in , and "</p><p>http://www.biomedcentral.com/1471-2180/8/60</p><p>BMC Microbiology 2008;8():60-60.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2374795.</p><p></p

Growth rates were determined from a fit to the exponential portion of the growth curve, extending in all but one case (, glucose minimal medium) through at least four mass doublings

Open symbols refer to growth in MOPS glucose plus required supplements (nicotinate, panthothenate and thiamine; see Methods), while closed symbols represent growth in MOPS glucose defined-rich medium. . growth rates. The values shown are the specific growth rate constants, , calculated as ln2/(doubling time, in h). For comparison, values of 0.5, 1, and 2 correspond respectively to doubling times of 83, 42, and 21 min. The rich medium results are clustered and therefore not labeled; for the minimal medium, the abbreviations used are Eco (), Pmi (), and Vch (). The diagonal line shows where points should fall if mutation has no effect on the growth rate in these media. . Complementation of the low growth rate in the glucose minimal medium described in (A). The dashed lines indicate growth data for the mutant (open circles; 193 min doubling time) and the mutant bearing the vector control (gray circles; 191 min). Remaining lines show the WT (closed circles; 66 min); and the mutant bearing plasmids with the genes from (triangles; 69 min), (squares; 81 min), or (diamonds; 81 min).<p><b>Copyright information:</b></p><p>Taken from "Limited functional conservation of a global regulator among related bacterial genera: Lrp in , and "</p><p>http://www.biomedcentral.com/1471-2180/8/60</p><p>BMC Microbiology 2008;8():60-60.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2374795.</p><p></p