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Low probability of initiating nirS transcription explains observed gas kinetics and growth of bacteria switching from aerobic respiration to denitrification.

Hassan J, Bergaust LL, Wheat ID, Bakken LR - PLoS Comput. Biol. (2014)

Bottom Line: The model is based on the hypothesis that nirS has a low probability (rden, h(-1)) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification.The resulting Fden (fraction of the cells recruited to denitrification) falls within 0.038-0.161.The phenomenon can be understood as a 'bet-hedging strategy': switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia turns out to be a 'false alarm'.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway.

ABSTRACT
In response to impending anoxic conditions, denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides (NOx) to N2 (denitrification). Since denitrifying bacteria are non-fermentative, the initial production of denitrification proteome depends on energy from aerobic respiration. Thus, if a cell fails to synthesise a minimum of denitrification proteome before O2 is completely exhausted, it will be unable to produce it later due to energy-limitation. Such entrapment in anoxia is recently claimed to be a major phenomenon in batch cultures of the model organism Paracoccus denitrificans on the basis of measured e(-)-flow rates to O2 and NOx. Here we constructed a dynamic model and explicitly simulated actual kinetics of recruitment of the cells to denitrification to directly and more accurately estimate the recruited fraction (Fden). Transcription of nirS is pivotal for denitrification, for it triggers a cascade of events leading to the synthesis of a full-fledged denitrification proteome. The model is based on the hypothesis that nirS has a low probability (rden, h(-1)) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification. We assume that the recruitment is initiated as [O2] falls below a critical threshold and terminates (assuming energy-limitation) as [O2] exhausts. With rden = 0.005 h(-1), the model robustly simulates observed denitrification kinetics for a range of culture conditions. The resulting Fden (fraction of the cells recruited to denitrification) falls within 0.038-0.161. In contrast, if the recruitment of the entire population is assumed, the simulated denitrification kinetics deviate grossly from those observed. The phenomenon can be understood as a 'bet-hedging strategy': switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia turns out to be a 'false alarm'.

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An overview of the modelled system: batch incubation in a gas-tight vial.The experiment: The stirred Sistrom's medium [27] was inoculated with aerobically grown Pa. denitrificans cells, which were provided with different concentrations of O2 and  (g or aq with a chemical species-name represents gaseous or aqueous, respectively). O2 is consumed by respiration, driving its transport from the headspace to the liquid. Once the aerobic respiration becomes limited, the cells may switch to denitrification (recruitment), reducing  to N2 via the intermediates NO and N2O (not shown). For monitoring O2, CO2, N2, NO and N2O, a robotised incubation system [28] was used, which automatically takes samples from the headspace by piercing the rubber septum. Each sampling removes a fraction (3–3.4%) of all gases in the headspace, but it also involves a marginal leakage of O2 and N2 into the vial (as indicated by the two-way arrows at the top of the figure). The model: The model operates with two sub-populations: one without and the other with denitrification enzymes ( and , respectively). Both consume O2 if present, but  cannot reduce NOx. The  cells may be recruited to the  pool as  falls below a critical threshold. The rate of recruitment () is modelled as a probabilistic function:  (cells h−1), where  represents an O2 dependent specific-probability (h−1) for any  cell to initiate nirS transcription (leading to the synthesis of a full-fledged denitrification proteome).
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pcbi-1003933-g003: An overview of the modelled system: batch incubation in a gas-tight vial.The experiment: The stirred Sistrom's medium [27] was inoculated with aerobically grown Pa. denitrificans cells, which were provided with different concentrations of O2 and (g or aq with a chemical species-name represents gaseous or aqueous, respectively). O2 is consumed by respiration, driving its transport from the headspace to the liquid. Once the aerobic respiration becomes limited, the cells may switch to denitrification (recruitment), reducing to N2 via the intermediates NO and N2O (not shown). For monitoring O2, CO2, N2, NO and N2O, a robotised incubation system [28] was used, which automatically takes samples from the headspace by piercing the rubber septum. Each sampling removes a fraction (3–3.4%) of all gases in the headspace, but it also involves a marginal leakage of O2 and N2 into the vial (as indicated by the two-way arrows at the top of the figure). The model: The model operates with two sub-populations: one without and the other with denitrification enzymes ( and , respectively). Both consume O2 if present, but cannot reduce NOx. The cells may be recruited to the pool as falls below a critical threshold. The rate of recruitment () is modelled as a probabilistic function: (cells h−1), where represents an O2 dependent specific-probability (h−1) for any cell to initiate nirS transcription (leading to the synthesis of a full-fledged denitrification proteome).

Mentions: Bergaust et al.[4], [8] studied aerobic and anaerobic respiration rates in Paracoccus denitrificans (DSM413). The cells were incubated (at 20°C) as stirred batches in 120 mL gastight vials, containing 50 mL Sistrom's medium [27] (Fig. 3). The medium was supplemented with various concentrations of KNO3 or KNO2. Prior to inoculation, air in the headspace was replaced with He to remove O2 and N2 (He-washing), followed by the injection of no, 1, or 7 headspace-vol.% O2. Finally, each vial was inoculated with ∼3×108 aerobically grown cells.


Low probability of initiating nirS transcription explains observed gas kinetics and growth of bacteria switching from aerobic respiration to denitrification.

Hassan J, Bergaust LL, Wheat ID, Bakken LR - PLoS Comput. Biol. (2014)

An overview of the modelled system: batch incubation in a gas-tight vial.The experiment: The stirred Sistrom's medium [27] was inoculated with aerobically grown Pa. denitrificans cells, which were provided with different concentrations of O2 and  (g or aq with a chemical species-name represents gaseous or aqueous, respectively). O2 is consumed by respiration, driving its transport from the headspace to the liquid. Once the aerobic respiration becomes limited, the cells may switch to denitrification (recruitment), reducing  to N2 via the intermediates NO and N2O (not shown). For monitoring O2, CO2, N2, NO and N2O, a robotised incubation system [28] was used, which automatically takes samples from the headspace by piercing the rubber septum. Each sampling removes a fraction (3–3.4%) of all gases in the headspace, but it also involves a marginal leakage of O2 and N2 into the vial (as indicated by the two-way arrows at the top of the figure). The model: The model operates with two sub-populations: one without and the other with denitrification enzymes ( and , respectively). Both consume O2 if present, but  cannot reduce NOx. The  cells may be recruited to the  pool as  falls below a critical threshold. The rate of recruitment () is modelled as a probabilistic function:  (cells h−1), where  represents an O2 dependent specific-probability (h−1) for any  cell to initiate nirS transcription (leading to the synthesis of a full-fledged denitrification proteome).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4222654&req=5

pcbi-1003933-g003: An overview of the modelled system: batch incubation in a gas-tight vial.The experiment: The stirred Sistrom's medium [27] was inoculated with aerobically grown Pa. denitrificans cells, which were provided with different concentrations of O2 and (g or aq with a chemical species-name represents gaseous or aqueous, respectively). O2 is consumed by respiration, driving its transport from the headspace to the liquid. Once the aerobic respiration becomes limited, the cells may switch to denitrification (recruitment), reducing to N2 via the intermediates NO and N2O (not shown). For monitoring O2, CO2, N2, NO and N2O, a robotised incubation system [28] was used, which automatically takes samples from the headspace by piercing the rubber septum. Each sampling removes a fraction (3–3.4%) of all gases in the headspace, but it also involves a marginal leakage of O2 and N2 into the vial (as indicated by the two-way arrows at the top of the figure). The model: The model operates with two sub-populations: one without and the other with denitrification enzymes ( and , respectively). Both consume O2 if present, but cannot reduce NOx. The cells may be recruited to the pool as falls below a critical threshold. The rate of recruitment () is modelled as a probabilistic function: (cells h−1), where represents an O2 dependent specific-probability (h−1) for any cell to initiate nirS transcription (leading to the synthesis of a full-fledged denitrification proteome).
Mentions: Bergaust et al.[4], [8] studied aerobic and anaerobic respiration rates in Paracoccus denitrificans (DSM413). The cells were incubated (at 20°C) as stirred batches in 120 mL gastight vials, containing 50 mL Sistrom's medium [27] (Fig. 3). The medium was supplemented with various concentrations of KNO3 or KNO2. Prior to inoculation, air in the headspace was replaced with He to remove O2 and N2 (He-washing), followed by the injection of no, 1, or 7 headspace-vol.% O2. Finally, each vial was inoculated with ∼3×108 aerobically grown cells.

Bottom Line: The model is based on the hypothesis that nirS has a low probability (rden, h(-1)) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification.The resulting Fden (fraction of the cells recruited to denitrification) falls within 0.038-0.161.The phenomenon can be understood as a 'bet-hedging strategy': switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia turns out to be a 'false alarm'.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway.

ABSTRACT
In response to impending anoxic conditions, denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides (NOx) to N2 (denitrification). Since denitrifying bacteria are non-fermentative, the initial production of denitrification proteome depends on energy from aerobic respiration. Thus, if a cell fails to synthesise a minimum of denitrification proteome before O2 is completely exhausted, it will be unable to produce it later due to energy-limitation. Such entrapment in anoxia is recently claimed to be a major phenomenon in batch cultures of the model organism Paracoccus denitrificans on the basis of measured e(-)-flow rates to O2 and NOx. Here we constructed a dynamic model and explicitly simulated actual kinetics of recruitment of the cells to denitrification to directly and more accurately estimate the recruited fraction (Fden). Transcription of nirS is pivotal for denitrification, for it triggers a cascade of events leading to the synthesis of a full-fledged denitrification proteome. The model is based on the hypothesis that nirS has a low probability (rden, h(-1)) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification. We assume that the recruitment is initiated as [O2] falls below a critical threshold and terminates (assuming energy-limitation) as [O2] exhausts. With rden = 0.005 h(-1), the model robustly simulates observed denitrification kinetics for a range of culture conditions. The resulting Fden (fraction of the cells recruited to denitrification) falls within 0.038-0.161. In contrast, if the recruitment of the entire population is assumed, the simulated denitrification kinetics deviate grossly from those observed. The phenomenon can be understood as a 'bet-hedging strategy': switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia turns out to be a 'false alarm'.

Show MeSH
Related in: MedlinePlus