Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions

Abstract

Although polycyclic aromatic hydrocarbons (PAHs) are harmful to human health, their elimination from the environment is not easy. Biodegradation of PAHs is promising since many bacteria have the ability to use hydrocarbons as their sole carbon and energy sources for growth. Of various microorganisms that can degrade PAHs, Pseudomonas aeruginosa is particularly important, not only because it causes a series of diseases including infection in cystic fibrosis patients, but also because it is a model bacterium in various studies. The genes that are responsible for degrading PAHs have been identified in P. aeruginosa, however, no gene acts alone as various stresses often initiate different metabolic pathways, quorum sensing, biofilm formation, antibiotic tolerance, etc. Therefore, it is important to study how PAH degradation genes behave under different conditions. In this study, we apply network analysis to investigating how 46 PAH degradation genes reorganized among 5549 genes in P. aeruginosa PAO1 under nine different conditions using publicly available gene coexpression data from GEO. The results provide six aspects of novelties: (i) comparing the number of gene clusters before and after stresses, (ii) comparing the membership in each gene cluster before and after stresses, (iii) defining which gene changed its membership together with PAH degradation genes before and after stresses, (iv) classifying membership-changed-genes in terms of category in Pseudomonas Genome Database, (v) postulating unknown gene's function, and (vi) proposing new mechanisms for genes of interests. This study can shed light on understanding of cooperative mechanisms of PAH degradation from the level of entire genes in an organism, and paves the way to conduct the similar studies on other genes.

Keywords: Bioinformatics; Network; Polycyclic aromatic hydrocarbon degradation gene; Pseudomonas Aeruginosa.

Fig. 1

Network of 5548 genes from P. aeruginosa PAO1 including 46 PAH degradation genes before (panel A) and after exposure (panel B) to hydrogen peroxide. Each symbol represents a gene with its code: circles represent non-PAH degradation genes and large triangles represent PAH degradation genes. Each edge represents a good correlation between two genes coexpression profiles. Because of space limitation, a cluster may not appear to contain many genes, but in reality, there are 521 genes in cyan cluster, 506 genes in yellow cluster, 398 genes in lime green cluster, 368 genes in red cluster, 361 genes in blue cluster, 356 genes in pink cluster, 343 genes in white cluster, 321 genes in orange cluster, 302 genes in purple cluster, 280 genes in cadet blue cluster, 253 genes in teal blue cluster, 252 genes in olive green cluster, 245 genes in gray cluster, 243 genes in black cluster, 225 genes in maroon cluster, 181 genes in light green cluster, 168 genes in light yellow cluster, 140 genes in magenta cluster, and 85 genes in midnight blue cluster in panel A. Panel C shows the genes together with PAH degradation genes found in new clusters after exposure to hydrogen peroxide in P. aeruginosa PAO1. Each pair of the following PAH degradation genes (PA0865 and PA4091, PA1205 and PA2217, PA2512 and PA4122, PA2515 and PA5427) have the same profiles

Fig. 1

Network of 5548 genes from P. aeruginosa PAO1 including 46 PAH degradation genes before (panel A) and after exposure (panel B) to hydrogen peroxide. Each symbol represents a gene with its code: circles represent non-PAH degradation genes and large triangles represent PAH degradation genes. Each edge represents a good correlation between two genes coexpression profiles. Because of space limitation, a cluster may not appear to contain many genes, but in reality, there are 521 genes in cyan cluster, 506 genes in yellow cluster, 398 genes in lime green cluster, 368 genes in red cluster, 361 genes in blue cluster, 356 genes in pink cluster, 343 genes in white cluster, 321 genes in orange cluster, 302 genes in purple cluster, 280 genes in cadet blue cluster, 253 genes in teal blue cluster, 252 genes in olive green cluster, 245 genes in gray cluster, 243 genes in black cluster, 225 genes in maroon cluster, 181 genes in light green cluster, 168 genes in light yellow cluster, 140 genes in magenta cluster, and 85 genes in midnight blue cluster in panel A. Panel C shows the genes together with PAH degradation genes found in new clusters after exposure to hydrogen peroxide in P. aeruginosa PAO1. Each pair of the following PAH degradation genes (PA0865 and PA4091, PA1205 and PA2217, PA2512 and PA4122, PA2515 and PA5427) have the same profiles

Fig. 2

Genes together with PAH degradation genes found in new clusters after exposure to sodium hypochlorite in P. aeruginosa PAO1. Each pair of the following PAH degradation genes have the same profiles: PA0230 and PA2518, PA0865 and PA0880, PA2083 and PA4486, PA2508 and PA2509, PA2514 and PA2546, PA3240 and PA4092, PA4121 and PA4122

Fig. 3

Gene networks of P. aeruginosa PAO1 after oxygen exposure from high to low oxygen concentration (upper panel) and from low to high oxygen concentration (lower panel)

Fig. 4

Genes together with PAH degradation genes found in new clusters before and after exposure to ortho-phenylphenol in P. aeruginosa PAO1 for 20 min (A) and for 60 min (B). In panel A, each pair of the following PAH degradation genes (PA0232 and PA4091, PA0247 and PA0817, PA0880 and PA2518, PA2507 and PA4121, PA2513 and PA4122, PA2514 and PA4123, PA3935 and PA4486) have the same profiles. In panel B, each pair of the following PAH degradation genes (PA0232 and PA4123, PA2217 and PA2516, PA2514 and PA4124, PA2518 and PA4486, PA2546 and PA4190) have the same profiles

Fig. 5

Genes together with PAH degradation genes found in new clusters before and after expression of RpoN (PA4462) molecular roadblock in P. aeruginosa PAO1. PA0817 and PA2217 have the same profiles

Fig. 6

Gene networks of the top 30 μm (upper panel) and bottom 30 μm (middle panel) of the P. aeruginosa PAO1 biofilms with PAH degradation genes (big symbols). Lower panel is gene compositions of the first five clusters (cluster 0 contains 1764 genes, cluster 1 contains 1730 genes, cluster 2 contains 1516 genes, cluster 3 contains 398 genes, cluster 4 contains 90 genes) in the bottom subpopulation of biofilms in terms of gene clusters in the top subpopulation of biofilms

Fig. 6

Gene networks of the top 30 μm (upper panel) and bottom 30 μm (middle panel) of the P. aeruginosa PAO1 biofilms with PAH degradation genes (big symbols). Lower panel is gene compositions of the first five clusters (cluster 0 contains 1764 genes, cluster 1 contains 1730 genes, cluster 2 contains 1516 genes, cluster 3 contains 398 genes, cluster 4 contains 90 genes) in the bottom subpopulation of biofilms in terms of gene clusters in the top subpopulation of biofilms

Fig. 7

Genes together with PAH degradation genes found in new clusters after 12 h treatments of the P. aeruginosa PAO1 biofilms with ciprofloxacin (left panel) and tobramycin (right panel). In left panel, each pair of the following PAH degradation genes (PA0232 and PA0880, PA0865 and PA2514, PA2024 and PA4486, PA2418 and PA3629) have the same profile, and three genes PA2083, PA2515, and PA4121 have the same profile. In the right panel, each pair of the following PAH degradation genes (PA0247 and PA2418, PA0865 and PA1205, PA2085 and PA5427) have the same profiles, and three genes PA0232, PA0880, and PA2517 have the same profile

Fig. 8

Genes together with PAH degradation genes found in new clusters of P. aeruginosa AES-1 (A) and AES-2 (B) in biofilm. In panel A, each pair of the following PAH degradation genes (PA2009 and PA3240, PA2514 and PA2517, PA2515 and PA3629, PA4123 and PA5427) have the same profiles, and the genes PA0154, PA0247, PA4121, and PA4122 have the same profiles. In panel B, each pair of the following PAH degradation genes (PA0153 and PA0865, PA0880 and PA2516, PA2508 and PA2509, PA3935 and PA4092, PA4091 and PA4122) have the same profiles

Fig. 9

Gene networks of wild-type P. aeruginosa PAO1 (upper panel) and PA2449-null mutant P. aeruginosa PW5126 (lower panel)

Fig. 10

Heatmap and cluster analysis of PAH degradation genes and their association with gene category in response to nine different stresses and conditions. Different colors in heatmap represent different numbers of genes in terms of gene category, and trees of dendrogram classify PAH degradation genes and gene category