Limits...
A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways.

Loriaux PM, Hoffmann A - PLoS Comput. Biol. (2013)

Bottom Line: In contrast, high flux of Mdm2 is not required for oscillations but preserves p53 sensitivity to sub-saturating doses of IR.In the NFκB system, degradation of NFκB-bound IκB by the IκB kinase (IKK) is required for activation in response to TNF, while high IKK-independent degradation prevents spurious activation in response to metabolic stress or low doses of TNF.Our work identifies flux pairs with opposing functional effects as a signaling motif that controls the stimulus-sensitivity of the p53 and NFκB stress-response pathways, and may constitute a general design principle in signaling pathways.

View Article: PubMed Central - PubMed

Affiliation: Signaling Systems Laboratory, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America.

ABSTRACT
Stimulus-induced perturbations from the steady state are a hallmark of signal transduction. In some signaling modules, the steady state is characterized by rapid synthesis and degradation of signaling proteins. Conspicuous among these are the p53 tumor suppressor, its negative regulator Mdm2, and the negative feedback regulator of NFκB, IκBα. We investigated the physiological importance of this turnover, or flux, using a computational method that allows flux to be systematically altered independently of the steady state protein abundances. Applying our method to a prototypical signaling module, we show that flux can precisely control the dynamic response to perturbation. Next, we applied our method to experimentally validated models of p53 and NFκB signaling. We find that high p53 flux is required for oscillations in response to a saturating dose of ionizing radiation (IR). In contrast, high flux of Mdm2 is not required for oscillations but preserves p53 sensitivity to sub-saturating doses of IR. In the NFκB system, degradation of NFκB-bound IκB by the IκB kinase (IKK) is required for activation in response to TNF, while high IKK-independent degradation prevents spurious activation in response to metabolic stress or low doses of TNF. Our work identifies flux pairs with opposing functional effects as a signaling motif that controls the stimulus-sensitivity of the p53 and NFκB stress-response pathways, and may constitute a general design principle in signaling pathways.

Show MeSH

Related in: MedlinePlus

A model of IκB-regulated NFκB activation.(A) An IκB-centric diagram of NFκB regulation. IκB is transcribed in an NFκB-dependent and -independent manner. Translated IκB may bind to IKK (cyan), NFκB (yellow), or both (green), or it may shuttle to the nucleus and bind to NFκB there. Degradation of IκB is possible from any state, though only when bound to IKK can degradation be enhanced by IKK activity. Activation of NFκB is achieved by the time-dependent numerical inputs  (magenta) and  (violet).  represents the activity of IKK kinase while  is the efficiency of mRNA translation. Both are defined over the interval , with  and  being their wildtype, unstimulated values. (B) The futile (red) and productive (blue) IκB degradation fluxes. The fraction of total IκB flux through each reaction is listed next to the corresponding reaction arrow. (C) Two stimuli used in our analysis of NFκB activation and the effects of IκB flux. Stimulation by TNF is modeled using the time-dependent IKK activation profile described in [29] and results in strong but transient activation of NFκB. Stimulation by UV is modeled as a 50% reduction of translational efficiency, as described in [13], and results in modest but sustained activation. As with p53, we define  and  to be the maximum activity of NFκB in response to TNF and UV, respectfully, and  to be the time at which  is observed. Because  is observed infinitely often, we define  to be the time at which NFκB activation reaches one-half .
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3585401&req=5

pcbi-1002932-g005: A model of IκB-regulated NFκB activation.(A) An IκB-centric diagram of NFκB regulation. IκB is transcribed in an NFκB-dependent and -independent manner. Translated IκB may bind to IKK (cyan), NFκB (yellow), or both (green), or it may shuttle to the nucleus and bind to NFκB there. Degradation of IκB is possible from any state, though only when bound to IKK can degradation be enhanced by IKK activity. Activation of NFκB is achieved by the time-dependent numerical inputs (magenta) and (violet). represents the activity of IKK kinase while is the efficiency of mRNA translation. Both are defined over the interval , with and being their wildtype, unstimulated values. (B) The futile (red) and productive (blue) IκB degradation fluxes. The fraction of total IκB flux through each reaction is listed next to the corresponding reaction arrow. (C) Two stimuli used in our analysis of NFκB activation and the effects of IκB flux. Stimulation by TNF is modeled using the time-dependent IKK activation profile described in [29] and results in strong but transient activation of NFκB. Stimulation by UV is modeled as a 50% reduction of translational efficiency, as described in [13], and results in modest but sustained activation. As with p53, we define and to be the maximum activity of NFκB in response to TNF and UV, respectfully, and to be the time at which is observed. Because is observed infinitely often, we define to be the time at which NFκB activation reaches one-half .

Mentions: Beginning with a published model of NFκB activation [13], we removed the beta and epsilon isoforms of IκB, leaving only the predominant isoform, IκBα (hereafter, simply “IκB”; Figure 5A). Steady state analysis of this model supported the observation that almost all IκB is degraded by either of two pathways: a “futile” flux, in which IκB is synthesized and degraded as an unbound monomer; and a “productive” flux, in which free IκB enters the nucleus and binds to NFκB, shuttles to the cytoplasm, then binds to and is targeted for degradation by IKK (Figure 5B). These two pathways account for 92.5% and 7.3% of the total IκB flux, respectively. The inflammatory stimulus TNF was modeled as before, using a numerically-defined IKK activity profile derived from in vitro kinase assays [30] (Figure 5A, variable ). Stimulating with TNF results in strong but transient activation of NFκB. A second stimulus, ribotoxic stress induced by UV irradiation, was modeled as 50% reduction in translation and results in only modest activity [13]. As above, we let be the amplitude of activated NFκB in response to TNF and the time at which is observed. Analogously, we let be the amplitude of NFκB in response to UV, and the time at which NFκB activation equals one-half (see Figure 5C). We then implemented multipliers for the futile and productive flux and let each multiplier take values on the interval . For each value we simulated the NFκB response to TNF and UV and plotted the effects on and .


A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways.

Loriaux PM, Hoffmann A - PLoS Comput. Biol. (2013)

A model of IκB-regulated NFκB activation.(A) An IκB-centric diagram of NFκB regulation. IκB is transcribed in an NFκB-dependent and -independent manner. Translated IκB may bind to IKK (cyan), NFκB (yellow), or both (green), or it may shuttle to the nucleus and bind to NFκB there. Degradation of IκB is possible from any state, though only when bound to IKK can degradation be enhanced by IKK activity. Activation of NFκB is achieved by the time-dependent numerical inputs  (magenta) and  (violet).  represents the activity of IKK kinase while  is the efficiency of mRNA translation. Both are defined over the interval , with  and  being their wildtype, unstimulated values. (B) The futile (red) and productive (blue) IκB degradation fluxes. The fraction of total IκB flux through each reaction is listed next to the corresponding reaction arrow. (C) Two stimuli used in our analysis of NFκB activation and the effects of IκB flux. Stimulation by TNF is modeled using the time-dependent IKK activation profile described in [29] and results in strong but transient activation of NFκB. Stimulation by UV is modeled as a 50% reduction of translational efficiency, as described in [13], and results in modest but sustained activation. As with p53, we define  and  to be the maximum activity of NFκB in response to TNF and UV, respectfully, and  to be the time at which  is observed. Because  is observed infinitely often, we define  to be the time at which NFκB activation reaches one-half .
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585401&req=5

pcbi-1002932-g005: A model of IκB-regulated NFκB activation.(A) An IκB-centric diagram of NFκB regulation. IκB is transcribed in an NFκB-dependent and -independent manner. Translated IκB may bind to IKK (cyan), NFκB (yellow), or both (green), or it may shuttle to the nucleus and bind to NFκB there. Degradation of IκB is possible from any state, though only when bound to IKK can degradation be enhanced by IKK activity. Activation of NFκB is achieved by the time-dependent numerical inputs (magenta) and (violet). represents the activity of IKK kinase while is the efficiency of mRNA translation. Both are defined over the interval , with and being their wildtype, unstimulated values. (B) The futile (red) and productive (blue) IκB degradation fluxes. The fraction of total IκB flux through each reaction is listed next to the corresponding reaction arrow. (C) Two stimuli used in our analysis of NFκB activation and the effects of IκB flux. Stimulation by TNF is modeled using the time-dependent IKK activation profile described in [29] and results in strong but transient activation of NFκB. Stimulation by UV is modeled as a 50% reduction of translational efficiency, as described in [13], and results in modest but sustained activation. As with p53, we define and to be the maximum activity of NFκB in response to TNF and UV, respectfully, and to be the time at which is observed. Because is observed infinitely often, we define to be the time at which NFκB activation reaches one-half .
Mentions: Beginning with a published model of NFκB activation [13], we removed the beta and epsilon isoforms of IκB, leaving only the predominant isoform, IκBα (hereafter, simply “IκB”; Figure 5A). Steady state analysis of this model supported the observation that almost all IκB is degraded by either of two pathways: a “futile” flux, in which IκB is synthesized and degraded as an unbound monomer; and a “productive” flux, in which free IκB enters the nucleus and binds to NFκB, shuttles to the cytoplasm, then binds to and is targeted for degradation by IKK (Figure 5B). These two pathways account for 92.5% and 7.3% of the total IκB flux, respectively. The inflammatory stimulus TNF was modeled as before, using a numerically-defined IKK activity profile derived from in vitro kinase assays [30] (Figure 5A, variable ). Stimulating with TNF results in strong but transient activation of NFκB. A second stimulus, ribotoxic stress induced by UV irradiation, was modeled as 50% reduction in translation and results in only modest activity [13]. As above, we let be the amplitude of activated NFκB in response to TNF and the time at which is observed. Analogously, we let be the amplitude of NFκB in response to UV, and the time at which NFκB activation equals one-half (see Figure 5C). We then implemented multipliers for the futile and productive flux and let each multiplier take values on the interval . For each value we simulated the NFκB response to TNF and UV and plotted the effects on and .

Bottom Line: In contrast, high flux of Mdm2 is not required for oscillations but preserves p53 sensitivity to sub-saturating doses of IR.In the NFκB system, degradation of NFκB-bound IκB by the IκB kinase (IKK) is required for activation in response to TNF, while high IKK-independent degradation prevents spurious activation in response to metabolic stress or low doses of TNF.Our work identifies flux pairs with opposing functional effects as a signaling motif that controls the stimulus-sensitivity of the p53 and NFκB stress-response pathways, and may constitute a general design principle in signaling pathways.

View Article: PubMed Central - PubMed

Affiliation: Signaling Systems Laboratory, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America.

ABSTRACT
Stimulus-induced perturbations from the steady state are a hallmark of signal transduction. In some signaling modules, the steady state is characterized by rapid synthesis and degradation of signaling proteins. Conspicuous among these are the p53 tumor suppressor, its negative regulator Mdm2, and the negative feedback regulator of NFκB, IκBα. We investigated the physiological importance of this turnover, or flux, using a computational method that allows flux to be systematically altered independently of the steady state protein abundances. Applying our method to a prototypical signaling module, we show that flux can precisely control the dynamic response to perturbation. Next, we applied our method to experimentally validated models of p53 and NFκB signaling. We find that high p53 flux is required for oscillations in response to a saturating dose of ionizing radiation (IR). In contrast, high flux of Mdm2 is not required for oscillations but preserves p53 sensitivity to sub-saturating doses of IR. In the NFκB system, degradation of NFκB-bound IκB by the IκB kinase (IKK) is required for activation in response to TNF, while high IKK-independent degradation prevents spurious activation in response to metabolic stress or low doses of TNF. Our work identifies flux pairs with opposing functional effects as a signaling motif that controls the stimulus-sensitivity of the p53 and NFκB stress-response pathways, and may constitute a general design principle in signaling pathways.

Show MeSH
Related in: MedlinePlus