Fig 1.
Expression of reference genes.
(A) Mean expression in total counts per million (TCPM) of 10 reference genes for each treatment/time point combination. The X-axis labels indicate the treatment and time point: “C” = control, “H” = 10 mg/L treatment, and “L” = 1 mg/L treatment. Expression values are the mean of three replicates. (B) Mean expression vs. coefficient of variation for 10 reference genes. Each point represents the mean expression of three replicates and the corresponding coefficient of variation for a treatment/time point combination. Gene abbreviations: cysG (siroheme synthase), gyrA (DNA gyrase, subunit A), hcaT (3-phenylpropionate transporter), idnT (L-Idonate transporter), pbpC (peptidoglycan glycosyltransferase), dapA (dihydrodipicolinate synthase), fucU (L-fucose mutarotase), hslV (heat-inducible protease subunit), mrdB (shape, elongation, division and sporulation family protein B), opgG (osmoregulated periplasmic glucans biosynthesis protein G).
Table 1.
Description of differentially expressed genes by time point and treatment.
FDR–False Discovery Rate corrected.
Fig 2.
Fold change in oxidative stress gene expression for 10-mg/L MCLR treatment.
Each point represents the log2 fold change relative to control at a given time point. The horizontal line at 0 represents equal expression in treatment and control. Gene abbreviations: acrA (multidrug efflux pump membrane fusion protein), ahpC (alkyl hydroperoxide reductase), gor (glutathione reductase), gstA (glutathione S-transferase), katG (catalase), nfsA (Nitroreductase A), sodA (Mn-containing superoxide dismutase), sodB (Fe-containing superoxide dismutase), sodC (Cu-Zn-containing superoxide dismutase).
Fig 3.
Fold change in envelope stress gene expression for 10-mg/L MCLR treatment.
(A) Genes of the σE regulon. (B) Genes of the Cpx regulon. Each point represents the log2 fold change relative to control at a given time point. The horizontal line at 0 represents equal expression in treatment and control. Gene abbreviations: degP (periplasmic serine endoprotease), dsbC (disulfide bond isomerase), fkpA (peptidyl-prolyl cis-trans isomerase), rpoD (RNA polymerase subunit, sigma 70), rpoE (RNA polymerase, sigma E), rpoH (RNA polymerase, sigma H), rseA (anti-RpoE sigma factor), rseP (intramembrane zinc metalloprotease), surA (peptidyl-prolyl cis-trans isomerase), yggN (DUF2884 family periplasmic protein), cpxA (sensory histidine kinase), cpxP (periplasmic adaptor protein), cpxR (DNA-binding transcriptional dual regulator), dsbA (protein disulfide oxidoreductase), spy (ATP-independent periplasmic chaperone), yebE (DUF533 family inner membrane protein), yiaF (DUF3053 domain-containing protein).