Fig 5. Genome-wide gene expression differences in P. veronii 1YdBTEX2 after 1 h exposure to different carbon sources or growth environment.

(A) Two-dimensional Principal Component Analysis of quadruplate global RNA-sequencing data sets of P. veronii 1YdBTEX2 incubated in liquid medium with succinate (Li-Su), or toluene (Li-To), or in sand with succinate (Sa-Su) or with toluene (Sa-To). (B) Venn diagram with the number of unique and common genes significantly differentially expressed (2-way ANOVA, ²log-fold-change [logFC] >1, false-discovery rate [FDR] <0.05, P <0.01) as result of change of carbon source (succinate to toluene) or environment (liquid to sand). (C) Smear-plot of global gene expression intensity (²log CPKM) versus expression changes (²log fold change) compared between cells incubated with toluene (Li-To) versus succinate (Li-Su); in grey, genes not statistically differentially expressed (logFC<1, FDR>0.05, P >0.01); magenta, genes with lower, and dark purple, genes with higher expression in presence of toluene (+). Blue, ipb genes; yellow, dmp genes; green, ttg genes (toluene efflux pump). (D) Gene expression changes as an effect of carbon source (succinate versus toluene, left) or of environment (liquid versus sand, right), and plotted as function of genomic location (chromosome 1, chr1; chromosome 2, chr2 and plasmid, plm; organized according to locus_tag number). Bars indicate ²log-fold change. Dark purple, statistically significantly higher expressed genes in presence of toluene (+, left) or sand (+, right); cyan, lower expressed genes in pink. Positions of the ipb, dmp and ttg genes are highlighted.