Ed the normalized values against every other (Figures 6A ; Tables S
Ed the normalized values against each and every other (Figures 6A ; Tables S6, S7). Most proteome and transcriptome fold-changes fall inside a factor of 2 in the diagonal, constant with concordant alterations in mRNA and protein and as a result limited post-transcriptional effects of aromatic inhibitors. A modest variety of RNA-protein pairs exhibited an 2-fold alter with p 0.05. For the duration of exponential phase, 4 proteins had been present at elevated levels relative to changes in RNA levels, which really decreased (RpoS, TnaA, MalE, and GlnH; red circles, Figure 6A; Table S7A), whereas 26 RNAs increased or decreased significantly with little difference in proteins levels (blue circles, Figure 6A; Table S7A). These disparate increases in RNA levels incorporated some of the key transcriptional responses for the Adenosine A2A receptor (A2AR) Species inhibitors (S assimilation plus the FrmA aldehyde detoxification pathway), and these proteins were present at high levels both with and without inhibitors (Table S7D). Many observations led us to conclude that these discrepancies in protein and RNA levels involving SynH2- and SynH2 cells reflect induction of expression in SynH2 cells but carryover of elevated protein levels inside the inoculum of SynH2- cells not however diluted in exponential phase. First, we sampled exponential phase between a single and two cell doublings so that proteins elevated in stationary phase in the inoculum may well nonetheless be present. Second, FrmRAB and S assimilation genes are elevated in stationary SynH2- cells relative to SynH2 cells (Table S7C), likely reflecting the greater accumulation of acetaldehyde in SynH2- cells in stationary phase (Figure 3C). Finally, RpoS and TnaA are markers of stationary phase (Lacour and Landini, 2004) and may well reflect elevation of these proteins in SynH stationary cells carried more than in the inoculum. In a similarFIGURE five | Growth phase-dependent alterations in inhibitor-responsive gene expression. Changes in RNA levels for genes that comprise the key regulatory response to aromatic inhibitors in SynH2. Shown are normalized RNA-seq measurements (top panel) from GLBRCE1 grown in SynH2 (solidlines) or SynH2- (dotted lines) or their relative ratios (bottom panel) from exponential, transition, and stationary phases of growth as indicated. (A) Aldehyde detoxification genes (frmA, frmB, dkgA, and yqhC). (B) Genes that encode efflux pumps (aaeA, aaeB, acrA, acrB).frontiersin.orgAugust 2014 | Volume 5 | Write-up 402 |Keating et al.Bacterial regulatory responses to lignocellulosic inhibitorsvein, the apparent overrepresentation of PyrBI, GadABC, and MetEF proteins in SynH2 cells could reflect their greater abundance in stationary phase SynH2 cells that have been carried over to early exponential phase. Supporting this view, transition phase cells in which the inoculum was diluted 5-fold exhibited a larger correlation amongst protein and RNA levels and only restricted proof of post-transcriptional regulation caused by the aromatic inhibitors (Figure 6B). Three clusters of outliers CXCR4 Biological Activity reflected (i) lowered transcript levels for S assimilation genes in SynH2- with no a corresponding drop in protein level (cys genes), (ii) larger levels of glnAGHLQ transcripts in SynH2 cells than SynH2- cells with high protein levels in both, and (iii) higher induction of transcripts for the citrate assimilation program (citDEFX) in SynH2 with lesser induction of protein levels. These effects likely reflect adjustment of S assimilation gene expression for the duration of transition phase, a higher induction of N assim.