Metabolic modelling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway
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 th...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2012-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2012.00370/full |
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| author | Marlies J. Kampschreur Marlies J. Kampschreur Robbert eKleerebezem Cristian ePicioreanu Lars Reier Bakken Linda eBergaust Simon ede Vries Mike S.M. Jetten Mike S.M. Jetten Mark C.M. Van Loosdrecht |
| author_facet | Marlies J. Kampschreur Marlies J. Kampschreur Robbert eKleerebezem Cristian ePicioreanu Lars Reier Bakken Linda eBergaust Simon ede Vries Mike S.M. Jetten Mike S.M. Jetten Mark C.M. Van Loosdrecht |
| author_sort | Marlies J. Kampschreur |
| collection | DOAJ |
| description | 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 modelled. 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 modelled are the inhibition of the cytochrome c oxidase by nitric oxide (NO), 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 unravelling the different factors involved in the complex response of A. tumefaciens to highly dynamic environmental conditions. |
| first_indexed | 2024-04-12T14:05:22Z |
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| id | doaj.art-6922f6b593734c93853f9f1b240bc53e |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-12T14:05:22Z |
| publishDate | 2012-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-6922f6b593734c93853f9f1b240bc53e2022-12-22T03:30:05ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2012-10-01310.3389/fmicb.2012.0037026331Metabolic modelling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathwayMarlies J. Kampschreur0Marlies J. Kampschreur1Robbert eKleerebezem2Cristian ePicioreanu3Lars Reier Bakken4Linda eBergaust5Simon ede Vries6Mike S.M. Jetten7Mike S.M. Jetten8Mark C.M. Van Loosdrecht9Delft University of TechnologyWaterboard Aa en MaasDelft University of TechnologyDelft University of TechnologyNorwegian University of Life SciencesNorwegian University of Life SciencesDelft University of TechnologyDelft University of TechnologyRadboud University NijmegenDelft University of TechnologyA 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 modelled. 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 modelled are the inhibition of the cytochrome c oxidase by nitric oxide (NO), 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 unravelling the different factors involved in the complex response of A. tumefaciens to highly dynamic environmental conditions.http://journal.frontiersin.org/Journal/10.3389/fmicb.2012.00370/fullAgrobacterium tumefaciensDenitrificationNitric OxideNitrous OxideMetabolic modelnitrite reduction |
| spellingShingle | Marlies J. Kampschreur Marlies J. Kampschreur Robbert eKleerebezem Cristian ePicioreanu Lars Reier Bakken Linda eBergaust Simon ede Vries Mike S.M. Jetten Mike S.M. Jetten Mark C.M. Van Loosdrecht Metabolic modelling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway Frontiers in Microbiology Agrobacterium tumefaciens Denitrification Nitric Oxide Nitrous Oxide Metabolic model nitrite reduction |
| title | Metabolic modelling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway |
| title_full | Metabolic modelling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway |
| title_fullStr | Metabolic modelling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway |
| title_full_unstemmed | Metabolic modelling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway |
| title_short | Metabolic modelling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway |
| title_sort | metabolic modelling of denitrification in agrobacterium tumefaciens a tool to study inhibiting and activating compounds for the denitrification pathway |
| topic | Agrobacterium tumefaciens Denitrification Nitric Oxide Nitrous Oxide Metabolic model nitrite reduction |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2012.00370/full |
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