Positions of acyl modification sites in RNA polymerase subunits.

<p>Location of acetylation (red line) and succinylation (blue line) sites with amino acid residue numbers are shown. K638, at which succinylation was reproducibly upregulated in the citrate condition, is underlined. Functional and structural regions are shown with black bars; the positions were estimated using amino acid sequence alignment and structural modeling based on information from <i>E</i>. <i>coli</i> RNAP [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131169#pone.0131169.ref060" target="_blank">60</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131169#pone.0131169.ref061" target="_blank">61</a>].</p

KEGG pathway enrichment for succinylated proteins in the glucose and citrate conditions.

<p>^aKEGG pathway term.</p><p>^bNumber of genes matching a given KEGG pathway term.</p><p>^cPercentage of genes matching a given term divided by the total number of input genes in each condition.</p><p>^dThe whole genome of <i>B</i>. <i>subtilis</i> was used as background. (An additional analysis performed using “the total <i>B</i>. <i>subtilis</i> proteins identified by MS from cell lysates” as background resulted in the same list of enrichment categories).</p><p>^eA Bonferroni cutoff value of 0.05 was used.</p><p>KEGG pathway enrichment for succinylated proteins in the glucose and citrate conditions.</p

The acetylome and succinylome of <i>Bacillus subtilis</i>.

<p>^aSites with an R-value >2-fold higher in glucose or sites specifically detected in glucose.</p><p>^bSites with an R-value >2-fold higher in citrate or sites specifically detected in citrate.</p><p>^cSites with an R-value with a fold change of <2.</p><p>^dSites that did not show a reproducible change.</p><p>The acetylome and succinylome of <i>Bacillus subtilis</i>.</p

Succinylation sites (42) upregulated in the citrate condition^a.

<p>^aSuccinylation sites that were reproducibly changed in the two experiments were chosen.</p><p>^bR-value (the ratio of glucose to citrate) is shown.</p><p>^cC, detected only in the citrate condition.</p><p>Succinylation sites (42) upregulated in the citrate condition<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131169#t006fn001" target="_blank">^a</a>.</p

Changes in <i>B</i>. <i>subtilis</i> lysine acetylation and succinylation in response to different carbon sources.

<p>Cells were grown in modified Spizizen’s minimal medium supplemented with glucose, citrate, glycerol, or pyruvate (30 mM) as the sole carbon source. Total lysates containing 20 μg of protein were separated by 10% SDS-PAGE. Left: Ponceau staining; right: western blot with anti-acetyl lysine (A) and anti-succinyl lysine (B) antibodies.</p

Changes in the acyl modification of central carbon metabolism proteins under glucose or citrate conditions.

<p>Red, blue, and green circles represent acetylated, succinylated, and overlapping sites, respectively. The number of circles represents the number of modification sites in each condition. Left, glucose condition; right, citrate condition.</p

<i>Bacillus subtilis</i> strains used in this study.

<p><i>Bacillus subtilis</i> strains used in this study.</p

KEGG pathway enrichment for acetylated proteins in the glucose and citrate conditions.

<p>^aKEGG pathway term.</p><p>^bNumber of genes matching a given KEGG pathway term.</p><p>^cPercentage of genes matching a given term divided by the total number of input genes in each condition.</p><p>^dThe whole genome of <i>B</i>. <i>subtilis</i> was used as background. (An additional analysis performed using “the total <i>B</i>. <i>subtilis</i> proteins identified by MS from cell lysates” as background resulted in the same list of enrichment categories.)</p><p>^eA Bonferroni cutoff value of 0.05 was used.</p><p>KEGG pathway enrichment for acetylated proteins in the glucose and citrate conditions.</p

The acetylome and succinylome of <i>B</i>. <i>subtilis</i> profiled in this study.

<p>(A) Functional classification of the identified acetylated proteins (629) and succinylated proteins (204) based on the KEGG pathway database. Red and blue bars represent the number of acetylated and succinylated proteins, respectively. (B) Overlap between acetylation (1355) and succinylation (327) sites. Red and blue circles enclose the number of acetylation and succinylation sites, respectively.</p

Acetylation sites upregulated in the glucose or citrate condition^a.

<p>^aAcetylation sites that were reproducibly changed in the two experiments were chosen.</p><p>^bR-value (the ratio of glucose to citrate) is shown.</p><p>^cG, detected only in the glucose condition; C, detected only in the citrate condition.</p><p>Acetylation sites upregulated in the glucose or citrate condition<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131169#t004fn001" target="_blank">^a</a>.</p