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A general model for toxin-antitoxin module dynamics can explain persister cell formation in E. coli.

Gelens L, Hill L, Vandervelde A, Danckaert J, Loris R - PLoS Comput. Biol. (2013)

Bottom Line: Conditional cooperativity and increasing the number of binding sites on the operator serves to reduce the metabolic burden of the cell by reducing the total amounts of proteins produced.The amplitude of these spikes determines the duration of the persister state.Finally, increases in the antitoxin degradation rate and decreases in the bacterial growth rate cause a rise in the amount of persisters during nutritional stress.

View Article: PubMed Central - PubMed

Affiliation: Applied Physics Research Group APHY, Vrije Universiteit Brussel, Brussels, Belgium. lendert.gelens@vub.ac.be

ABSTRACT
Toxin-Antitoxin modules are small operons involved in stress response and persister cell formation that encode a "toxin" and its corresponding neutralizing "antitoxin". Regulation of these modules involves a complex mechanism known as conditional cooperativity, which is supposed to prevent unwanted toxin activation. Here we develop mathematical models for their regulation, based on published molecular and structural data, and parameterized using experimental data for F-plasmid ccdAB, bacteriophage P1 phd/doc and E. coli relBE. We show that the level of free toxin in the cell is mainly controlled through toxin sequestration in toxin-antitoxin complexes of various stoichiometry rather than by gene regulation. If the toxin translation rate exceeds twice the antitoxin translation rate, toxins accumulate in all cells. Conditional cooperativity and increasing the number of binding sites on the operator serves to reduce the metabolic burden of the cell by reducing the total amounts of proteins produced. Combining conditional cooperativity and bridging of antitoxins by toxins when bound to their operator sites allows creation of persister cells through rare, extreme stochastic spikes in the free toxin level. The amplitude of these spikes determines the duration of the persister state. Finally, increases in the antitoxin degradation rate and decreases in the bacterial growth rate cause a rise in the amount of persisters during nutritional stress.

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Related in: MedlinePlus

Numerical simulation of the generic TA model including two independent binding sites.The systems were simulated for 500 minutes per individual cell. The graphs show the results for a single cell (color-coded towards the species plotted: free antitoxin (green), free toxin (red), AT complex (dark blue), TAT complex (cyan) or free operator DNA (gray)) as well as an average of 1000 cells (in black). The used parameter sets are indicated above the panels. No toxic feedback effects are included: .
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pcbi-1003190-g002: Numerical simulation of the generic TA model including two independent binding sites.The systems were simulated for 500 minutes per individual cell. The graphs show the results for a single cell (color-coded towards the species plotted: free antitoxin (green), free toxin (red), AT complex (dark blue), TAT complex (cyan) or free operator DNA (gray)) as well as an average of 1000 cells (in black). The used parameter sets are indicated above the panels. No toxic feedback effects are included: .

Mentions: In order to determine the influence of the parameter set used on the behavior of the toxin-antitoxin module, we performed stochastic simulations of a toxin-antitoxin module with two independent antitoxin binding sites on the promoter/operator, and the parameter sets for the ccdAB, phd/doc and relBE system (see Table 1 and Figure 2). Initially, mRNA is transcribed and toxin and antitoxin are translated (Figure 2A and B) as the operator DNA is initially unbound (Figure 2E). Once the operator gets bound, repression starts and mRNA transcription stops. From Figure 2E, it can be seen that after this initial response, the operator DNA is mostly occupied by one or more protein species. Pulses in the toxin and antitoxin level occur during short periods when the operator becomes unoccupied in a single cell. The free toxin population is retained at very low levels as is expected in a growing cell population [17]. For the relBE system, a maximum of eight free toxins is found for the simulated cell shown in Figure 2 and the average free toxin level is approximately one, whereas for the ccdAB and phd/doc systems, the average free toxin level is much lower than one (Figure 2B). The overall majority of toxin molecules are thus sequestered into toxin-antitoxin complexes AT (Figure 2C) or TAT (Figure 2D).


A general model for toxin-antitoxin module dynamics can explain persister cell formation in E. coli.

Gelens L, Hill L, Vandervelde A, Danckaert J, Loris R - PLoS Comput. Biol. (2013)

Numerical simulation of the generic TA model including two independent binding sites.The systems were simulated for 500 minutes per individual cell. The graphs show the results for a single cell (color-coded towards the species plotted: free antitoxin (green), free toxin (red), AT complex (dark blue), TAT complex (cyan) or free operator DNA (gray)) as well as an average of 1000 cells (in black). The used parameter sets are indicated above the panels. No toxic feedback effects are included: .
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3757116&req=5

pcbi-1003190-g002: Numerical simulation of the generic TA model including two independent binding sites.The systems were simulated for 500 minutes per individual cell. The graphs show the results for a single cell (color-coded towards the species plotted: free antitoxin (green), free toxin (red), AT complex (dark blue), TAT complex (cyan) or free operator DNA (gray)) as well as an average of 1000 cells (in black). The used parameter sets are indicated above the panels. No toxic feedback effects are included: .
Mentions: In order to determine the influence of the parameter set used on the behavior of the toxin-antitoxin module, we performed stochastic simulations of a toxin-antitoxin module with two independent antitoxin binding sites on the promoter/operator, and the parameter sets for the ccdAB, phd/doc and relBE system (see Table 1 and Figure 2). Initially, mRNA is transcribed and toxin and antitoxin are translated (Figure 2A and B) as the operator DNA is initially unbound (Figure 2E). Once the operator gets bound, repression starts and mRNA transcription stops. From Figure 2E, it can be seen that after this initial response, the operator DNA is mostly occupied by one or more protein species. Pulses in the toxin and antitoxin level occur during short periods when the operator becomes unoccupied in a single cell. The free toxin population is retained at very low levels as is expected in a growing cell population [17]. For the relBE system, a maximum of eight free toxins is found for the simulated cell shown in Figure 2 and the average free toxin level is approximately one, whereas for the ccdAB and phd/doc systems, the average free toxin level is much lower than one (Figure 2B). The overall majority of toxin molecules are thus sequestered into toxin-antitoxin complexes AT (Figure 2C) or TAT (Figure 2D).

Bottom Line: Conditional cooperativity and increasing the number of binding sites on the operator serves to reduce the metabolic burden of the cell by reducing the total amounts of proteins produced.The amplitude of these spikes determines the duration of the persister state.Finally, increases in the antitoxin degradation rate and decreases in the bacterial growth rate cause a rise in the amount of persisters during nutritional stress.

View Article: PubMed Central - PubMed

Affiliation: Applied Physics Research Group APHY, Vrije Universiteit Brussel, Brussels, Belgium. lendert.gelens@vub.ac.be

ABSTRACT
Toxin-Antitoxin modules are small operons involved in stress response and persister cell formation that encode a "toxin" and its corresponding neutralizing "antitoxin". Regulation of these modules involves a complex mechanism known as conditional cooperativity, which is supposed to prevent unwanted toxin activation. Here we develop mathematical models for their regulation, based on published molecular and structural data, and parameterized using experimental data for F-plasmid ccdAB, bacteriophage P1 phd/doc and E. coli relBE. We show that the level of free toxin in the cell is mainly controlled through toxin sequestration in toxin-antitoxin complexes of various stoichiometry rather than by gene regulation. If the toxin translation rate exceeds twice the antitoxin translation rate, toxins accumulate in all cells. Conditional cooperativity and increasing the number of binding sites on the operator serves to reduce the metabolic burden of the cell by reducing the total amounts of proteins produced. Combining conditional cooperativity and bridging of antitoxins by toxins when bound to their operator sites allows creation of persister cells through rare, extreme stochastic spikes in the free toxin level. The amplitude of these spikes determines the duration of the persister state. Finally, increases in the antitoxin degradation rate and decreases in the bacterial growth rate cause a rise in the amount of persisters during nutritional stress.

Show MeSH
Related in: MedlinePlus