Figure 1.

Comparative analysis of PAO1, ΔdksA1, ΔdksA2, and ΔdksA1ΔdksA2 transcriptomes. Transcript levels of genes (indicated to the left in B–I) were quantified by row Z-score (A) and represented as heat maps (B–I). The row Z-score was calculated by log₂-transformed RPKM values of targeted genes. The formula to calculate row Z-scores from RPKM values was log₂(RPKM + 1). The row Z-score value ranges from −1.5 to 1.5 and is represented as a color-coded box, with red and blue indicating relative up-regulation and down-regulation, respectively. B, transcript levels of genes encoding 50S ribosomal protein components. C, transcript levels of genes encoding 30S ribosomal protein components. D, transcript levels of genes encoding 16S and 23S ribosomal protein components. E, transcription of genes involved in QS and QS-regulated virulence determinants. Expression of rhlI and PQS synthesis genes was significantly decreased in ΔdksA1 and ΔdksA1ΔdksA2 mutants. Genes encoding elastase (lasB), rhamnolipid (rhlA and rhlB), pyochelin (pchR–pchG), phenazine (phzA1 and phzB1), alkaline protease (aprA–aprF), and the type 2 secretion system (xcpZ–xcpQ) were down-regulated in the presence of dksA1 gene mutation. F, transcription of genes involved in polyamine metabolism. Genes encoding proteins for polyamine biosynthesis and polyamine catabolism were differentially regulated in the absence of DksA1. G, transcription of genes encoding reductase for nitrate reductase (Nar), nitrite reductase (Nir), nitric oxide reductase (Nor), and nitrous oxide reductase (Nos) were down-regulated in dksA1 mutants. Expression of genes encoding positive regulators NarX, NarL, and DNR was increased. Transcription of genes involved in flagella synthesis and assembly (H) and type IV pili synthesis (I).