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 (NO₂), nitric oxide (NO) and nitrous oxide (N₂O). 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 (O₂), nitrate (NO₃), and phosphate (PO₄) suggests that PO₄ 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 PO₄ on a denitrification metabolic network of P. aeruginosa in order to shed light on mechanisms for greenhouse gas N₂O 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 Lakemore »
- Authors:
-
- Virginia Tech, Blacksburg, VA (United States)
- Bowling Green State Univ., Bowling Green, OH (United States)
- Univ. of Connecticut Health Center, Farmington, CT (United States); Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
- Publication Date:
- Research Org.:
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1188326
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 2; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES
Citation Formats
Arat, Seda, Bullerjahn, George S., and Laubenbacher, Reinhard. A network biology approach to denitrification in Pseudomonas aeruginosa. United States: N. p., 2015.
Web. doi:10.1371/journal.pone.0118235.
Arat, Seda, Bullerjahn, George S., & Laubenbacher, Reinhard. A network biology approach to denitrification in Pseudomonas aeruginosa. United States. https://doi.org/10.1371/journal.pone.0118235
Arat, Seda, Bullerjahn, George S., and Laubenbacher, Reinhard. Mon .
"A network biology approach to denitrification in Pseudomonas aeruginosa". United States. https://doi.org/10.1371/journal.pone.0118235. https://www.osti.gov/servlets/purl/1188326.
@article{osti_1188326,
title = {A network biology approach to denitrification in Pseudomonas aeruginosa},
author = {Arat, Seda and Bullerjahn, George S. and Laubenbacher, Reinhard},
abstractNote = {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 (NO₂), nitric oxide (NO) and nitrous oxide (N₂O). 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 (O₂), nitrate (NO₃), and phosphate (PO₄) suggests that PO₄ 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 PO₄ on a denitrification metabolic network of P. aeruginosa in order to shed light on mechanisms for greenhouse gas N₂O 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.},
doi = {10.1371/journal.pone.0118235},
journal = {PLoS ONE},
number = 2,
volume = 10,
place = {United States},
year = {Mon Feb 23 00:00:00 EST 2015},
month = {Mon Feb 23 00:00:00 EST 2015}
}
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Metabolic modeling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway
journal, January 2012
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