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.Electronic supplementary materialThe online version of this article (doi:10.1007/s13353-017-0402-9) contains supplementary material, which is available to authorized users.

Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

“…Such intermediates are then converted, through β-ketoadipate pathway, to citric acid cycle (CAC) intermediates [ 88 ]. Gentisate, homogentisate, and homoprotocatechuate represent other metabolic routes, whose genes have been described in metagenomes and trascriptomes belonging to Pseudomonas aeruginosa PAO1, Klesbiella Pneumoniae AWD5, and within a bacteria consortium composed by Pseudomonas , Aquabacterium , Chryseobacterium , Sphingobium , Novosphingobium , Dokdonella , Parvibaculum, and Achromobacter [ 89 , 90 , 91 ]. The cytochrome P450-mediated pathway is a further metabolic pathway used by bacteria to degrade PAHs, which leads to the production of trans-dihydrodiols [ 92 ].…”

Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium

“…The degradation capacity of our strain was measured connected to phenanthrene and naphthalene and after one week of incubation it was not detectable. It is assumed that the isolation environment (not contaminated by aromatic compounds) of the strain plays direct role in these results, however, the genes for the possible degradation of aromatic compounds could be activated after a long time exposure [57,58].…”

Metagenomics and Metatranscriptomics Suggest Pathways of 3-Chloroaniline Degradation in Wastewater Reactors

“…Metagenomic and metatranscriptomic analyses allow the examination of differential gene enrichment and transcription respectively, in complex microbial communities like activated sludge. Some researchers have used transcriptomics approaches to elucidate degradation pathways via gene transcription in aromatics degradation in pure culture experiments (Tam et al, 2006;Yan and Wu, 2017;Cauduro et al, 2020;Ma et al, 2020b).…”

“…Metagenomic and metatranscriptomic analyses allow the examination of differential gene enrichment and transcription respectively, in complex microbial communities like activated sludge. Some researchers have used transcriptomics approaches to elucidate degradation pathways via gene transcription in aromatics degradation in pure culture experiments (Tam et al ., 2006; Yan and Wu, 2017; Cauduro et al ., 2020; Ma et al ., 2020b). Long-term metatranscriptomics sampling has also helped show differential enrichment and transcription of aromatics degradation genes in activated sludge bioreactors (Sato et al ., 2019; Sun et al ., 2019; Yu et al ., 2019).…”