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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 during experiment with 1% gas phase oxygen and 1mM nitrite. (A) Gas phase concentrations of O2 (♦), NO (•), and N2O (Δ). (B) Liquid concentrations of N2O (), O2 (), nitrite (×, ), and NO (). (C) Liquid concentrations of expressed nir (), measured nirK mRNA (○), expressed nor (), measured norB mRNA (ρ), 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 = 0.99, R2 NO = 0.80, R2 N2O = 0.93, R2 CO2 = 0.97 with .
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Figure 3: Modeled (lines) and measured (points) concentrations during experiment with 1% gas phase oxygen and 1mM nitrite. (A) Gas phase concentrations of O2 (♦), NO (•), and N2O (Δ). (B) Liquid concentrations of N2O (), O2 (), nitrite (×, ), and NO (). (C) Liquid concentrations of expressed nir (), measured nirK mRNA (○), expressed nor (), measured norB mRNA (ρ), 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 = 0.99, R2 NO = 0.80, R2 N2O = 0.93, R2 CO2 = 0.97 with .

Mentions: The induction of NO reductase expression by NO in A. tumefaciens, was previously shown (Baek and Shapleigh, 2005). The activation of norB transcription by NO can be deduced from panel A2 in Figure 2, where norB transcripts appear as soon as NO is measured. However, NO concentrations are very low, meaning that the affinity for NO is very high. These observations suggest that nitrite activates nirK transcription and NO stimulates norB transcription, which leads to a satisfactory model fit for the reference experiment (Figure 3). However, as indicated before, the enzyme synthesis parameters could not accurately be identified due to limited experimental data during the transition period. The maximum rate of transcription of norB is higher than the transcription rate for nirK. This can clearly be seen from the rapid increase in norB concentration after NO is detected, while nirK increases slower despite continuous nitrite presence.


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 during experiment with 1% gas phase oxygen and 1mM nitrite. (A) Gas phase concentrations of O2 (♦), NO (•), and N2O (Δ). (B) Liquid concentrations of N2O (), O2 (), nitrite (×, ), and NO (). (C) Liquid concentrations of expressed nir (), measured nirK mRNA (○), expressed nor (), measured norB mRNA (ρ), 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 = 0.99, R2 NO = 0.80, R2 N2O = 0.93, R2 CO2 = 0.97 with .
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Modeled (lines) and measured (points) concentrations during experiment with 1% gas phase oxygen and 1mM nitrite. (A) Gas phase concentrations of O2 (♦), NO (•), and N2O (Δ). (B) Liquid concentrations of N2O (), O2 (), nitrite (×, ), and NO (). (C) Liquid concentrations of expressed nir (), measured nirK mRNA (○), expressed nor (), measured norB mRNA (ρ), 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 = 0.99, R2 NO = 0.80, R2 N2O = 0.93, R2 CO2 = 0.97 with .
Mentions: The induction of NO reductase expression by NO in A. tumefaciens, was previously shown (Baek and Shapleigh, 2005). The activation of norB transcription by NO can be deduced from panel A2 in Figure 2, where norB transcripts appear as soon as NO is measured. However, NO concentrations are very low, meaning that the affinity for NO is very high. These observations suggest that nitrite activates nirK transcription and NO stimulates norB transcription, which leads to a satisfactory model fit for the reference experiment (Figure 3). However, as indicated before, the enzyme synthesis parameters could not accurately be identified due to limited experimental data during the transition period. The maximum rate of transcription of norB is higher than the transcription rate for nirK. This can clearly be seen from the rapid increase in norB concentration after NO is detected, while nirK increases slower despite continuous nitrite presence.

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