Plots comparing the log₂ expression ratios of the arginine deiminase (ADI) and enterococcal biofilm associated pilus (Ebp) operons in DBS01.

<p>Plots comparing the log₂ expression ratios of the arginine deiminase (ADI) and enterococcal biofilm associated pilus (Ebp) operons in DBS01.</p

Platelet binding activity of E99 and DBS01.

<p>The values shown are percent of wild-type (E99) binding (mean ± SD). Differences in platelet binding efficiencies were determined using an unpaired <i>t</i>-test (P = 0.05). Platelet binding assays were performed in triplicate and each experiment was repeated thrice (n = 9).</p

Members of the PerA regulon confirmed by qRT-PCR.

*<p>Change in DBS01 gene expression (DBS01 : E99) at OD600 = 0.05, 0.5 and 1.0.</p><p>Experiments were repeated twice, with 3 replicates for each gene per assay. Mean values shown (standard error in parenthesis).</p

All genes differently regulated in DBS01 mapped onto the <i>E. faecalis</i> chromosome.

<p>The outer ring displays those genes differentially regulated during mid-exponential phase. The middle ring displays those genes differentially regulated during late-exponential phase. The inner ring displays those genes differentially regulated during stationary phase. The innermost circle displays the location relative to position zero in millions of base pairs of the <i>E. faecalis</i> V583 genome. The locations of the arginine deiminase (ADI) and enterococcal biofilm-associated pilus (Ebp) operons, the <i>E. faecalis</i> pathogenicity island (PAI), and a phage related element are indicated.</p

Map of <i>E. faecalis</i> V583 phage 04.

<p>The putative proteins were compiled using the annotated V583 sequence. The direction of transcription is shown in blue (reverse) and red (forward). Heat maps of expression ratios (fold change) for DBS01 are shown for mid-exponential (O.D. 600 = 0.05), late-exponential (O.D. 600 = 0.5) and stationary phase (O.D. 600 = 1.0).</p

Comparisons of microarray results for E99 and DBS01.

<p>Control RNA was extracted from E99 and used to normalize the test RNA extracted from DBS01 (DBS01 : E99). All data presented here are shown as fold change in gene expression (test : control). (A) Upper diagram: Venn diagram comparing significantly up-regulated genes (>2 fold) in DBS01 during mid-exponential, late-exponential and stationary phase. Lower diagram: Venn diagram comparing significantly down-regulated genes (>2 fold) in DBS01 during mid-exponential, late-exponential, and stationary phase. (B) Hierarchically-clustered heat map of all genes differentially regulated>twofold between DBS01 and E99.</p

<i>perA, ebpR-ebpABC</i> and <i>bps</i> gene expression in E99 grown in THB supplemented with 100 mM sodium bicarbonate (dark bars) or DBS01 grown in THB (light bars).

<p>Microarray assays were performed twice. The values shown are mean expression intensities (mean ± SD) of biological replicates. Fold changes in gene expression were calculated by comparing E99 grown in THB to E99 grown in THB+100 mM sodium bicarbonate and by comparing DBS01 grown in THB to E99 grown in THB.</p

Bacterial strains and plasmids used in this study.

1<p>Str^R, streptomycin resistance; Nal^R, nalidixic acid resistance; Rif^R, rifampicin resistance; Amp^R, ampicillin resistance; T^S, temperature sensitive replication.</p

Phenotypic assay results for <i>E. coli</i> HS mutants.

<p><b>A–L.</b> Biolog GN2 (Gram negative carbon nutrition) plates were utilized to assess the overall metabolic capacity of the mutants constructed in <i>E. coli</i> HS to consume 95 individual carbon sources (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053957#s4" target="_blank">Materials and Methods</a> for details). The kinetic curves plot substrate oxidation vs. time. Green represents carbon source utilization by the <i>E. coli</i> HS wild type strain, red represents the mutant strain, and yellow represents utilization by both strains. Mutant strains of <i>E. coli</i> HS: (<b>A</b>) Δ<i>araBAD</i>, (<b>B</b>) <i>araBAD+</i>, (<b>C</b>) Δ<i>galK</i>, (<b>D</b>) <i>galK+</i>, (<b>E</b>) Δ<i>fucK</i>, (<b>F</b>) Δ<i>gntK</i> Δ<i>idnK</i>, (<b>G</b>) Δ<i>lacZ</i>, (<b>H</b>) Δ<i>manA</i>, (<b>I</b>) Δ<i>nagE</i>, (<b>J</b>) Δ<i>nanAT</i>, (<b>K</b>) Δ<i>rbsK</i>, and (<b>L</b>) Δ<i>uxaC</i>. <b>M.</b> Sugar utilization was assessed in minimal media containing 0.2% carbon source. The final O.D.₆₀₀'s following 12 hour incubations are shown. Note: the generation time of <i>E. coli HS</i> Δ<i>nagE</i> on N-acetylglucosamine is 2.6 h compared to 1 h for the wild type (see text for details). The sugars N-acetylneuraminate and ribose are not represented on the Biolog plate (NA).</p

<i>E. coli</i> HS sugar utilization in the mouse intestine.

<p>The difference between population density of the wild type and each mutant strain is shown at Day 1 and Day 9, plus or minus the standard error of the mean. Significant values (bold) indicate log difference >0.8 and student's <i>t</i> test value P<0.05 at Day 9.</p