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Metabolic modeling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway.

Kampschreur MJ, Kleerebezem R, Picioreanu C, Bakken L, Bergaust L, de Vries S, Jetten MS, van Loosdrecht MC - Front Microbiol (2012)

Bottom Line: The objective of this work was to study the key factors regulating the metabolic response of the denitrification pathway to transition from oxic to anoxic respiration and to find parameter values for the biological processes that were modeled.The metabolic model was used to test hypotheses that were formulated based on the experimental results and offers a structured look on the processes that occur in the cell during transition in respiration.The main phenomena that were modeled are the inhibition of the cytochrome c oxidase by nitric oxide (NO) and the (indirect) inhibition of oxygen on the denitrification enzymes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Delft University of Technology Delft, Netherlands.

ABSTRACT
A metabolic network model for facultative denitrification was developed based on experimental data obtained with Agrobacterium tumefaciens. The model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. The objective of this work was to study the key factors regulating the metabolic response of the denitrification pathway to transition from oxic to anoxic respiration and to find parameter values for the biological processes that were modeled. The metabolic model was used to test hypotheses that were formulated based on the experimental results and offers a structured look on the processes that occur in the cell during transition in respiration. The main phenomena that were modeled are the inhibition of the cytochrome c oxidase by nitric oxide (NO) and the (indirect) inhibition of oxygen on the denitrification enzymes. The activation of transcription of nitrite reductase and NO reductase by their respective substrates were hypothesized. The general assumption that nitrite and NO reduction are controlled interdependently to prevent NO accumulation does not hold for A. tumefaciens. The metabolic network model was demonstrated to be a useful tool for unraveling the different factors involved in the complex response of A. tumefaciens to highly dynamic environmental conditions.

No MeSH data available.


Related in: MedlinePlus

Modeled (lines) and measured (points) concentrations when extrapolating the metabolic model to the experiment with 1% gas phase oxygen and 1 mM nitrate. (A) Gas phase concentrations of O2 (♦), NO (•), and N2O (Δ). (B) Liquid concentrations of N2O (), O2 (), nitrate (), nitrite (×, ), and NO (). (C) Liquid concentrations of expressed nap (– –), expressed nir (), measured nirK mRNA (○), expressed nor (), measured norB mRNA (Δ), and biomass (). (D) Gas phase concentration of CO2 (□). The fit between the modeled data and the experimental data was assessed using the R2-value: R2 O2 = 0.98, R2 NO = –0.29, R2 N2O = 0.85, R2 CO2 = 0.80 with . The negative R2 for NO is caused by the poor description of the experimental NO concentrations by the model. Consequently, the sum of squared errors for the model description was larger than the sum of the variance of the experimental values.
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Figure 4: Modeled (lines) and measured (points) concentrations when extrapolating the metabolic model to the experiment with 1% gas phase oxygen and 1 mM nitrate. (A) Gas phase concentrations of O2 (♦), NO (•), and N2O (Δ). (B) Liquid concentrations of N2O (), O2 (), nitrate (), nitrite (×, ), and NO (). (C) Liquid concentrations of expressed nap (– –), expressed nir (), measured nirK mRNA (○), expressed nor (), measured norB mRNA (Δ), and biomass (). (D) Gas phase concentration of CO2 (□). The fit between the modeled data and the experimental data was assessed using the R2-value: R2 O2 = 0.98, R2 NO = –0.29, R2 N2O = 0.85, R2 CO2 = 0.80 with . The negative R2 for NO is caused by the poor description of the experimental NO concentrations by the model. Consequently, the sum of squared errors for the model description was larger than the sum of the variance of the experimental values.

Mentions: The metabolic model is based on the experiment with 1% oxygen gas phase and 1 mM nitrite as initial concentrations. Subsequently, the model was extrapolated to the experiment with 1% oxygen gas phase and 1 mM nitrate as initial concentrations. When modeling the nitrate experiment, the parameters identified in the nitrite experiment were used and only new parameters were added for the reduction of nitrate to nitrite. The modeled behavior of the oxygen uptake and N2O and CO2 production showed a relatively good correlation with the experimental data but the modeled NO concentrations were much lower than the measured NO concentrations (see Figure 4). This is further discussed in the model limitations section (“Model Limitations and Outlook”).


Metabolic modeling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway.

Kampschreur MJ, Kleerebezem R, Picioreanu C, Bakken L, Bergaust L, de Vries S, Jetten MS, van Loosdrecht MC - Front Microbiol (2012)

Modeled (lines) and measured (points) concentrations when extrapolating the metabolic model to the experiment with 1% gas phase oxygen and 1 mM nitrate. (A) Gas phase concentrations of O2 (♦), NO (•), and N2O (Δ). (B) Liquid concentrations of N2O (), O2 (), nitrate (), nitrite (×, ), and NO (). (C) Liquid concentrations of expressed nap (– –), expressed nir (), measured nirK mRNA (○), expressed nor (), measured norB mRNA (Δ), and biomass (). (D) Gas phase concentration of CO2 (□). The fit between the modeled data and the experimental data was assessed using the R2-value: R2 O2 = 0.98, R2 NO = –0.29, R2 N2O = 0.85, R2 CO2 = 0.80 with . The negative R2 for NO is caused by the poor description of the experimental NO concentrations by the model. Consequently, the sum of squared errors for the model description was larger than the sum of the variance of the experimental values.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475394&req=5

Figure 4: Modeled (lines) and measured (points) concentrations when extrapolating the metabolic model to the experiment with 1% gas phase oxygen and 1 mM nitrate. (A) Gas phase concentrations of O2 (♦), NO (•), and N2O (Δ). (B) Liquid concentrations of N2O (), O2 (), nitrate (), nitrite (×, ), and NO (). (C) Liquid concentrations of expressed nap (– –), expressed nir (), measured nirK mRNA (○), expressed nor (), measured norB mRNA (Δ), and biomass (). (D) Gas phase concentration of CO2 (□). The fit between the modeled data and the experimental data was assessed using the R2-value: R2 O2 = 0.98, R2 NO = –0.29, R2 N2O = 0.85, R2 CO2 = 0.80 with . The negative R2 for NO is caused by the poor description of the experimental NO concentrations by the model. Consequently, the sum of squared errors for the model description was larger than the sum of the variance of the experimental values.
Mentions: The metabolic model is based on the experiment with 1% oxygen gas phase and 1 mM nitrite as initial concentrations. Subsequently, the model was extrapolated to the experiment with 1% oxygen gas phase and 1 mM nitrate as initial concentrations. When modeling the nitrate experiment, the parameters identified in the nitrite experiment were used and only new parameters were added for the reduction of nitrate to nitrite. The modeled behavior of the oxygen uptake and N2O and CO2 production showed a relatively good correlation with the experimental data but the modeled NO concentrations were much lower than the measured NO concentrations (see Figure 4). This is further discussed in the model limitations section (“Model Limitations and Outlook”).

Bottom Line: The objective of this work was to study the key factors regulating the metabolic response of the denitrification pathway to transition from oxic to anoxic respiration and to find parameter values for the biological processes that were modeled.The metabolic model was used to test hypotheses that were formulated based on the experimental results and offers a structured look on the processes that occur in the cell during transition in respiration.The main phenomena that were modeled are the inhibition of the cytochrome c oxidase by nitric oxide (NO) and the (indirect) inhibition of oxygen on the denitrification enzymes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Delft University of Technology Delft, Netherlands.

ABSTRACT
A metabolic network model for facultative denitrification was developed based on experimental data obtained with Agrobacterium tumefaciens. The model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. The objective of this work was to study the key factors regulating the metabolic response of the denitrification pathway to transition from oxic to anoxic respiration and to find parameter values for the biological processes that were modeled. The metabolic model was used to test hypotheses that were formulated based on the experimental results and offers a structured look on the processes that occur in the cell during transition in respiration. The main phenomena that were modeled are the inhibition of the cytochrome c oxidase by nitric oxide (NO) and the (indirect) inhibition of oxygen on the denitrification enzymes. The activation of transcription of nitrite reductase and NO reductase by their respective substrates were hypothesized. The general assumption that nitrite and NO reduction are controlled interdependently to prevent NO accumulation does not hold for A. tumefaciens. The metabolic network model was demonstrated to be a useful tool for unraveling the different factors involved in the complex response of A. tumefaciens to highly dynamic environmental conditions.

No MeSH data available.


Related in: MedlinePlus