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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

Measured nirK and norB transcription together with concentrations of nitrate, nitrite, N2O, and O2 in time. (A) Experiment with 1% gas phase oxygen and 1 mM nitrite: nitrite (×), NirK (○), NORB (◊) NO (□), oxygen (∆). (B) Experiment with 1% gas phase oxygen and 1 mM nitrate; nitrite (×), NirK (•), NORB (♦), NO (■), oxygen (▲). Due to required amount of biomass for PCR analysis these experiments comprised several parallel flasks, see Bergaust et al. (2008) for details about the experiments.
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Figure 2: Measured nirK and norB transcription together with concentrations of nitrate, nitrite, N2O, and O2 in time. (A) Experiment with 1% gas phase oxygen and 1 mM nitrite: nitrite (×), NirK (○), NORB (◊) NO (□), oxygen (∆). (B) Experiment with 1% gas phase oxygen and 1 mM nitrate; nitrite (×), NirK (•), NORB (♦), NO (■), oxygen (▲). Due to required amount of biomass for PCR analysis these experiments comprised several parallel flasks, see Bergaust et al. (2008) for details about the experiments.

Mentions: Based on the experimental data of Bergaust et al. (2008) it was hypothesized that the transcription of nirK is activated by its substrate nitrite. This could be identified based on the experiments at 1% initial oxygen in the gas phase combined with 1 mM nitrite or nitrate (Figure 2). The substrate concentration dependency of nirK transcription was modeled using saturation kinetics. In the nitrite experiment, nirK is rapidly transcribed from the start. The maximum specific nirK transcription rate was identified by the increase in nirK mRNA at non-limiting nitrite concentration (first 20 h in Figure 2). In the nitrate experiment nirK is only transcribed when the nitrite concentration has increased after nitrate reduction is initiated. The affinity constant for nitrite of nirK transcription (see Table 1) was deduced from the data obtained from the nitrate experiment (Figure 2, panel B). Here it can be seen that nirK transcription increases upon the increase in nitrite concentration.


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)

Measured nirK and norB transcription together with concentrations of nitrate, nitrite, N2O, and O2 in time. (A) Experiment with 1% gas phase oxygen and 1 mM nitrite: nitrite (×), NirK (○), NORB (◊) NO (□), oxygen (∆). (B) Experiment with 1% gas phase oxygen and 1 mM nitrate; nitrite (×), NirK (•), NORB (♦), NO (■), oxygen (▲). Due to required amount of biomass for PCR analysis these experiments comprised several parallel flasks, see Bergaust et al. (2008) for details about the experiments.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Measured nirK and norB transcription together with concentrations of nitrate, nitrite, N2O, and O2 in time. (A) Experiment with 1% gas phase oxygen and 1 mM nitrite: nitrite (×), NirK (○), NORB (◊) NO (□), oxygen (∆). (B) Experiment with 1% gas phase oxygen and 1 mM nitrate; nitrite (×), NirK (•), NORB (♦), NO (■), oxygen (▲). Due to required amount of biomass for PCR analysis these experiments comprised several parallel flasks, see Bergaust et al. (2008) for details about the experiments.
Mentions: Based on the experimental data of Bergaust et al. (2008) it was hypothesized that the transcription of nirK is activated by its substrate nitrite. This could be identified based on the experiments at 1% initial oxygen in the gas phase combined with 1 mM nitrite or nitrate (Figure 2). The substrate concentration dependency of nirK transcription was modeled using saturation kinetics. In the nitrite experiment, nirK is rapidly transcribed from the start. The maximum specific nirK transcription rate was identified by the increase in nirK mRNA at non-limiting nitrite concentration (first 20 h in Figure 2). In the nitrate experiment nirK is only transcribed when the nitrite concentration has increased after nitrate reduction is initiated. The affinity constant for nitrite of nirK transcription (see Table 1) was deduced from the data obtained from the nitrate experiment (Figure 2, panel B). Here it can be seen that nirK transcription increases upon the increase in nitrite concentration.

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