A Network Biology Approach to Denitrification in Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa is a metabolically flexible member of the Gammaproteobacteria. Under anaerobic conditions and the presence of nitrate, P. aeruginosa can perform (complete) denitrification, a respiratory process of dissimilatory nitrate reduction to nitrogen gas via nitrite (NO 2), nitric oxide (NO) and nitrous oxide (N 2 O). This study focuses on understanding the influence of environmental conditions on bacterial denitrification performance, using a mathematical model of a metabolic network in P. aeruginosa. To our knowledge, this is the first mathematical model of denitrification for this bacterium. Analysis of the long-term behavior of the network under changing concentration levels of oxygen (O 2), nitrate (NO 3), and phosphate (PO 4) suggests that PO 4 concentration strongly affects denitrification performance. The model provides three predictions on denitrification activity of P. aeruginosa under various environmental conditions, and these predictions are either experimentally validated or supported by pertinent biological literature. One motivation for this study is to capture the effect of PO 4 on a denitrification metabolic network of P. aeruginosa in order to shed light on mechanisms for greenhouse gas N 2 O accumulation during seasonal oxygen depletion in aquatic environments such as Lake Erie (Laurentian Great Lakes, USA). Simulating the microbial production of greenhouse gases in anaerobic aquatic systems such as Lake Erie allows a deeper understanding of the contributing environmental effects that will inform studies on, and remediation strategies for, other hypoxic sites worldwide.

Environmentally controlled bacterial vesicle-mediated export

“…Most studies of OMV production in P. aeruginosa use aerobically focused on monitoring OMV production under denitrifying conditions (Toyofuku et al, 2013). P. aeruginosa undergo anaerobic respiration via denitrification, utilizing nitrates or oxidized forms of nitrogen (Arai, 2011;Arat, Bullerjahn, & Laubenbacher, 2015). This is particularly relevant during biofilm growth, due to the generation of anaerobic microenvironments because of inherent oxygen gradients within the biofilm (Xu, Stewart, Xia, Huang, & McFeters, 1998;Werner et al, 2004).…”

An integrated network analysis reveals that nitric oxide reductase prevents metabolic cycling of nitric oxide by Pseudomonas aeruginosa

“…aeruginosa and NO, a previous mathematical model of the regulatory network associated with denitrification was developed by Arat and colleagues [44]. In that study, a qualitative, discretevariable model of the P. aeruginosa denitrification regulatory network was constructed to understand the impact of environmental variables, such as phosphate and O 2 , on the system [44].…”

“…S1) [61]. These three transcription factors and their regulatory interactions were also included in the P. aeruginosa regulatory network constructed by Arat and colleagues [44]; however, the present implementation enables quantitative analysis of time-dependent changes in this pathway, and does so in the context of a larger, more expansive network.…”

Changes in Denitrification Potentials and Riverbank Soil Bacterial Structures along Shibetsu River, Japan

“…Gammaproteobacteria is also known as a metabolically flexible group of bacteria; thus, they perform denitrification only when conditions are favourable. For example, the lack of phosphorus is known as a factor controlling the denitrification performance of a group of Gammaproteobacteria [41]. us, in future, we should observe the availability of nutrients other than C and N to fully understand the factors controlling the denitrification potentials of riverbank soils.…”