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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

Scheme of conversions and regulation of denitrification pathway in Agrobacterium tumefaciens as used in the metabolic model of the experiments. The combination of experimental data and the metabolic model led to identification of nirK and norB transcription activated by their substrates, nap transcription by oxygen limitation, apparent (indirect, via electron transport chain) oxygen inhibition of the denitrification conversions and NO inhibition on the cytochrome c oxidase. The processes that were modeled are: (1) oxygen reduction, (2) nitrate reductase synthesis, (3) nitrate reduction, (4) nitrite reductase synthesis, (5) nitrite reduction, (6) NO reductase synthesis, (7) NO reduction.
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Figure 1: Scheme of conversions and regulation of denitrification pathway in Agrobacterium tumefaciens as used in the metabolic model of the experiments. The combination of experimental data and the metabolic model led to identification of nirK and norB transcription activated by their substrates, nap transcription by oxygen limitation, apparent (indirect, via electron transport chain) oxygen inhibition of the denitrification conversions and NO inhibition on the cytochrome c oxidase. The processes that were modeled are: (1) oxygen reduction, (2) nitrate reductase synthesis, (3) nitrate reduction, (4) nitrite reductase synthesis, (5) nitrite reduction, (6) NO reductase synthesis, (7) NO reduction.

Mentions: The model developed considers that A. tumefaciens converts succinate (electron donor and carbon source) with oxygen (aerobic respiration) or with nitrate, nitrite, and NO (denitrification steps). In the experiments denitrification rates are changing over time due to availability of electron acceptors (O2, nitrate, nitrite, and NO) and varying enzyme concentrations. Consequently, denitrification is described in the metabolic model by two levels of cellular organization: (1) enzyme expression (in which DNA transcription and translation are lumped) and (2) enzyme activity leading to substrate conversion and microbial growth. The lumping of transcription and translation means that the model assumes that the rate of enzyme production is proportional to the mRNA level and that the response time for enzyme translation is insignificant. It is further assumed that the translation rate is equal for nap-, nirK-, and norB-transcripts. This simplification led to a good description of the reference experiment but could be responsible for the poor extrapolation of the model to other experiments. A scheme of the conversions and regulation factors of the denitrification pathway in A. tumefaciens as used in the metabolic model is shown in Figure 1.


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)

Scheme of conversions and regulation of denitrification pathway in Agrobacterium tumefaciens as used in the metabolic model of the experiments. The combination of experimental data and the metabolic model led to identification of nirK and norB transcription activated by their substrates, nap transcription by oxygen limitation, apparent (indirect, via electron transport chain) oxygen inhibition of the denitrification conversions and NO inhibition on the cytochrome c oxidase. The processes that were modeled are: (1) oxygen reduction, (2) nitrate reductase synthesis, (3) nitrate reduction, (4) nitrite reductase synthesis, (5) nitrite reduction, (6) NO reductase synthesis, (7) NO reduction.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Scheme of conversions and regulation of denitrification pathway in Agrobacterium tumefaciens as used in the metabolic model of the experiments. The combination of experimental data and the metabolic model led to identification of nirK and norB transcription activated by their substrates, nap transcription by oxygen limitation, apparent (indirect, via electron transport chain) oxygen inhibition of the denitrification conversions and NO inhibition on the cytochrome c oxidase. The processes that were modeled are: (1) oxygen reduction, (2) nitrate reductase synthesis, (3) nitrate reduction, (4) nitrite reductase synthesis, (5) nitrite reduction, (6) NO reductase synthesis, (7) NO reduction.
Mentions: The model developed considers that A. tumefaciens converts succinate (electron donor and carbon source) with oxygen (aerobic respiration) or with nitrate, nitrite, and NO (denitrification steps). In the experiments denitrification rates are changing over time due to availability of electron acceptors (O2, nitrate, nitrite, and NO) and varying enzyme concentrations. Consequently, denitrification is described in the metabolic model by two levels of cellular organization: (1) enzyme expression (in which DNA transcription and translation are lumped) and (2) enzyme activity leading to substrate conversion and microbial growth. The lumping of transcription and translation means that the model assumes that the rate of enzyme production is proportional to the mRNA level and that the response time for enzyme translation is insignificant. It is further assumed that the translation rate is equal for nap-, nirK-, and norB-transcripts. This simplification led to a good description of the reference experiment but could be responsible for the poor extrapolation of the model to other experiments. A scheme of the conversions and regulation factors of the denitrification pathway in A. tumefaciens as used in the metabolic model is shown in Figure 1.

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