Cross-regulatory network in Pseudomonas aeruginosa biofilm genes and TiO2 anatase induced molecular perturbations in key proteins unraveled by a systems biology approach

A systems biology approach was used to study all the biofilm related genes of P. aeruginosa PAO1, and the interaction of titanium dioxide (TiO2) anatase with biofilm related proteins. Among the 71 genes, the interactions of all the nodal pairs were extracted by STRING 10.5 database. The inter-relationship among these genes was predicted by constructing complete PPI network and visualized in Cytoscape v 3.4.0. Total number of nodes of the network was found to be 335 and edges were 795. The network was further investigated for its clusters and the best cluster was further analyzed for the hub proteins which significantly contribute in cross-regulation of the biofilm related process. The hub proteins were identified based on four topological parameters of degree, closeness, betweeness and radiality. Four major hub proteins of P. aeruginosa PAO1 were identified to be algD, gacS, rpoS and rpoN which were common in all the hubs. Further, we have also elucidated the probable mechanism of TiO2 interaction with P. aeruginosa PAO1 at molecular level. Using STITCH server, the major target gene of TiO2 was identified as katA which also appeared commonly in our main dataset and this gene has been focused for the further study because of its unique common appearance in gene-gene network as well as gene-anatase network. The direct interacting partners of katA were found to be dnaK, hfq, rpoS and rpoA. Based on these findings and available gene regulatory information, probable TiO2 interacting cascade has been represented. This in silico study of P. aeruginosa PAO1 biofilm genes and the interaction of protein products with TiO2 might be significant to understand the perspective pathogenic resistance as well as the toxicity research pertaining to nanoparticles.