Figure 1.
Schematic representation of a biofilm.
This figure shows a schematic alignment of a biofilm and how nutrition and oxygen varies depending on the position of P. aeruginosa (PAO1) within the biofilm. From top to bottom and from the edge to the middle, the oxygen concentration decreases. The nutrient supply is more limited at the bottom and in the middle than on the top and at the boundaries of the biofilm. The redox potential also decreases from top to bottom. The pH value and endogenous nutrient concentrations thus vary according to the position of PA in the biofilm. The colonies PAO1_1.1 and PAO1_1.3 have the highest oxygen and nutrient supply, while for PAO1_3.2, these factors are most limited.
Table 1.
This table lists all genes, which abolished PA growth in a single gene deletion and which had no homologous genes in the human genome.
Table 2.
Oxygen-sensitive genes.
Figure 2.
Essential genes for biomass precursor synthesis.
This figure shows the results of the single gene deletion study, where the 398 candidate drug target genes are listed along the y-axis and the biomass precursors found in the biomass reaction [29] are listed on the x-axis. The color scale shows biomass precursor synthesis ability with zero corresponding to a complete loss of the precursor synthesis capability. Interesting areas in the four plots are highlighted with red boxes and discussed further in the text. Box A shows genes, which were essential in minimal but not in rich media. Box B corresponds to the area of amino acid precursors. We can see that in rich media the gene deletion had an effect on amino acid precursors but was not essential compared to minimal media, in which the gene deletion was essential. Box C highlights genes with subsystem effect. Box D shows those genes, which have a global effect but differed between minimal and rich media conditions. Box E shows similar tendency but a global effect is only observed in rich media conditions while gene deletion had a moderate effect in minimal media conditions. The arrows point to i) some few examples of single effect of gene deletion or ii) genes, whose deletion affected only a single precursor.
Figure 3.
This figure shows the results of the double gene deletion study. White background corresponds to rich media and gray to minimal media. The diagram in the left hand side compare oxygen rich and the right hand side compares oxygen poor conditions. Red cells indicate essential double knockout combinations.