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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

Oxygen influence on NO reduction activity; oxygen (♦), NO (•), and N2O (∆) concentrations during experiment with 13% initial gas phase oxygen and 0.2 mM nitrite. Oxygen addition is performed after 43 h and leads to immediate increase in NO reduction, as identified from NO decrease and N2O increase.
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FA3: Oxygen influence on NO reduction activity; oxygen (♦), NO (•), and N2O (∆) concentrations during experiment with 13% initial gas phase oxygen and 0.2 mM nitrite. Oxygen addition is performed after 43 h and leads to immediate increase in NO reduction, as identified from NO decrease and N2O increase.

Mentions: Additional experiments were performed in 120 ml serum flasks, containing 50 ml Sistrom's medium (see Bergaust et al., 2008) with 34 mM succinate as the only C source and different concentrations of KNO2. The initial oxygen concentration in the headspace was increased to 13% oxygen in the headspace. Inocula of fully dispersed, aerobically grown, late exponential cells of Agrobacterium tumefaciens, which had not been previously exposed to anoxic conditions, were injected into the flasks. When oxygen depletion occurred, oxygen was added again to the headspace of the flasks. Figure A3, shows an example of an experiment in which after oxygen addition NO reduction rates increased.


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)

Oxygen influence on NO reduction activity; oxygen (♦), NO (•), and N2O (∆) concentrations during experiment with 13% initial gas phase oxygen and 0.2 mM nitrite. Oxygen addition is performed after 43 h and leads to immediate increase in NO reduction, as identified from NO decrease and N2O increase.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

FA3: Oxygen influence on NO reduction activity; oxygen (♦), NO (•), and N2O (∆) concentrations during experiment with 13% initial gas phase oxygen and 0.2 mM nitrite. Oxygen addition is performed after 43 h and leads to immediate increase in NO reduction, as identified from NO decrease and N2O increase.
Mentions: Additional experiments were performed in 120 ml serum flasks, containing 50 ml Sistrom's medium (see Bergaust et al., 2008) with 34 mM succinate as the only C source and different concentrations of KNO2. The initial oxygen concentration in the headspace was increased to 13% oxygen in the headspace. Inocula of fully dispersed, aerobically grown, late exponential cells of Agrobacterium tumefaciens, which had not been previously exposed to anoxic conditions, were injected into the flasks. When oxygen depletion occurred, oxygen was added again to the headspace of the flasks. Figure A3, shows an example of an experiment in which after oxygen addition NO reduction rates increased.

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