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Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network.

Axelrod K, Sanchez A, Gore J - Elife (2015)

Bottom Line: This loss of resilience was observed for perturbations that interact directly with the gene circuit as well as for a variety of generic perturbations-such as salt, ethanol, or temperature shocks-that alter the state of the cell more broadly.We obtain qualitatively similar findings in natural gene circuits, such as the yeast GAL network.Our findings illustrate how phenotypic memory can become destabilized by environmental variability near a critical transition.

View Article: PubMed Central - PubMed

Affiliation: Harvard University, Graduate Program in Biophysics, Cambridge, United States.

ABSTRACT
Microorganisms often exhibit a history-dependent phenotypic response after exposure to a stimulus which can be imperative for proper function. However, cells frequently experience unexpected environmental perturbations that might induce phenotypic switching. How cells maintain phenotypic states in the face of environmental fluctuations remains an open question. Here, we use environmental perturbations to characterize the resilience of phenotypic states in a synthetic gene network near a critical transition. We find that far from the critical transition an environmental perturbation may induce little to no phenotypic switching, whereas close to the critical transition the same perturbation can cause many cells to switch phenotypic states. This loss of resilience was observed for perturbations that interact directly with the gene circuit as well as for a variety of generic perturbations-such as salt, ethanol, or temperature shocks-that alter the state of the cell more broadly. We obtain qualitatively similar findings in natural gene circuits, such as the yeast GAL network. Our findings illustrate how phenotypic memory can become destabilized by environmental variability near a critical transition.

No MeSH data available.


Related in: MedlinePlus

Increasing the strength of a generic perturbation increases the probability that cells will switch into the alternative phenotypic state.Yeast cells expressing the toggle switch were pre-grown in a high GFP state and then transferred to an environmental condition that is close to the phenotypic switch ([ATc] = 8 ng/ml). Cells were perturbed for 24 hr with a salt (upper panel) or an ethanol pulse (lower panel) and then allowed to recover for 24 hr. The fraction of cells that switch into the high RFP state in response to the perturbation is plotted as a function of perturbation intensity. ATc and IPTG were held fixed throughout the perturbation and recovery periods. Control cells were propagated with no supplemental salt or ethanol for comparison. Error bars represent the standard error of measurements from three different gatings on FSC-A vs SSC-A.DOI:http://dx.doi.org/10.7554/eLife.07935.010
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fig3s1: Increasing the strength of a generic perturbation increases the probability that cells will switch into the alternative phenotypic state.Yeast cells expressing the toggle switch were pre-grown in a high GFP state and then transferred to an environmental condition that is close to the phenotypic switch ([ATc] = 8 ng/ml). Cells were perturbed for 24 hr with a salt (upper panel) or an ethanol pulse (lower panel) and then allowed to recover for 24 hr. The fraction of cells that switch into the high RFP state in response to the perturbation is plotted as a function of perturbation intensity. ATc and IPTG were held fixed throughout the perturbation and recovery periods. Control cells were propagated with no supplemental salt or ethanol for comparison. Error bars represent the standard error of measurements from three different gatings on FSC-A vs SSC-A.DOI:http://dx.doi.org/10.7554/eLife.07935.010

Mentions: Cellular memory in development and cell cycle progression must be resilient against a wide range of different environmental perturbations. Given this, we wanted to explore whether memory in the toggle switch would lose resilience against generic perturbations approaching a critical transition. Cells from a high GFP history at different distances from the phenotypic switch (2, 4, and 8 ng/ml ATc) were perturbed in several different ways for 24 hr: heat stress, osmotic stress with sodium chloride, ethanol stress, and a glucose pulse. Remarkably, we observed a loss of resilience against all four of these generic perturbations (Figure 3A,B). Far from the critical transition (2 ng/ml ATc), there was little to no phenotypic switching in response to any of these ‘generic’ perturbations. However, close to the critical transition (8 ng/ml ATc) we observed nearly complete switching in all perturbations, despite the fact that there was essentially no switching (∼0.5%) in the absence of the perturbations. At a given distance from the phenotypic switch, increasing the strength of a generic perturbation increased the probability that cells would switch into the alternative state (Figure 3—figure supplement 1). The switching induced by the glucose perturbation can perhaps be understood by the fact that glucose shuts down expression of the entire system (LacI, TetR, GFP, and RFP) via catabolite repression of a GAL1 upstream activation sequence, thus pushing the cells toward a low GFP and low RFP state (Gardner et al., 2000; Ellis et al., 2009). The other three perturbations have much broader effects on the cell with no obvious connection to the toggle switch network being probed in our experiments. Cellular memory can therefore degrade near a critical transition for a wide range of different environmental perturbations (Figure 3C).10.7554/eLife.07935.009Figure 3.Cellular memory of the high GFP history in the toggle switch loses resilience to generic perturbations.


Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network.

Axelrod K, Sanchez A, Gore J - Elife (2015)

Increasing the strength of a generic perturbation increases the probability that cells will switch into the alternative phenotypic state.Yeast cells expressing the toggle switch were pre-grown in a high GFP state and then transferred to an environmental condition that is close to the phenotypic switch ([ATc] = 8 ng/ml). Cells were perturbed for 24 hr with a salt (upper panel) or an ethanol pulse (lower panel) and then allowed to recover for 24 hr. The fraction of cells that switch into the high RFP state in response to the perturbation is plotted as a function of perturbation intensity. ATc and IPTG were held fixed throughout the perturbation and recovery periods. Control cells were propagated with no supplemental salt or ethanol for comparison. Error bars represent the standard error of measurements from three different gatings on FSC-A vs SSC-A.DOI:http://dx.doi.org/10.7554/eLife.07935.010
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4547091&req=5

fig3s1: Increasing the strength of a generic perturbation increases the probability that cells will switch into the alternative phenotypic state.Yeast cells expressing the toggle switch were pre-grown in a high GFP state and then transferred to an environmental condition that is close to the phenotypic switch ([ATc] = 8 ng/ml). Cells were perturbed for 24 hr with a salt (upper panel) or an ethanol pulse (lower panel) and then allowed to recover for 24 hr. The fraction of cells that switch into the high RFP state in response to the perturbation is plotted as a function of perturbation intensity. ATc and IPTG were held fixed throughout the perturbation and recovery periods. Control cells were propagated with no supplemental salt or ethanol for comparison. Error bars represent the standard error of measurements from three different gatings on FSC-A vs SSC-A.DOI:http://dx.doi.org/10.7554/eLife.07935.010
Mentions: Cellular memory in development and cell cycle progression must be resilient against a wide range of different environmental perturbations. Given this, we wanted to explore whether memory in the toggle switch would lose resilience against generic perturbations approaching a critical transition. Cells from a high GFP history at different distances from the phenotypic switch (2, 4, and 8 ng/ml ATc) were perturbed in several different ways for 24 hr: heat stress, osmotic stress with sodium chloride, ethanol stress, and a glucose pulse. Remarkably, we observed a loss of resilience against all four of these generic perturbations (Figure 3A,B). Far from the critical transition (2 ng/ml ATc), there was little to no phenotypic switching in response to any of these ‘generic’ perturbations. However, close to the critical transition (8 ng/ml ATc) we observed nearly complete switching in all perturbations, despite the fact that there was essentially no switching (∼0.5%) in the absence of the perturbations. At a given distance from the phenotypic switch, increasing the strength of a generic perturbation increased the probability that cells would switch into the alternative state (Figure 3—figure supplement 1). The switching induced by the glucose perturbation can perhaps be understood by the fact that glucose shuts down expression of the entire system (LacI, TetR, GFP, and RFP) via catabolite repression of a GAL1 upstream activation sequence, thus pushing the cells toward a low GFP and low RFP state (Gardner et al., 2000; Ellis et al., 2009). The other three perturbations have much broader effects on the cell with no obvious connection to the toggle switch network being probed in our experiments. Cellular memory can therefore degrade near a critical transition for a wide range of different environmental perturbations (Figure 3C).10.7554/eLife.07935.009Figure 3.Cellular memory of the high GFP history in the toggle switch loses resilience to generic perturbations.

Bottom Line: This loss of resilience was observed for perturbations that interact directly with the gene circuit as well as for a variety of generic perturbations-such as salt, ethanol, or temperature shocks-that alter the state of the cell more broadly.We obtain qualitatively similar findings in natural gene circuits, such as the yeast GAL network.Our findings illustrate how phenotypic memory can become destabilized by environmental variability near a critical transition.

View Article: PubMed Central - PubMed

Affiliation: Harvard University, Graduate Program in Biophysics, Cambridge, United States.

ABSTRACT
Microorganisms often exhibit a history-dependent phenotypic response after exposure to a stimulus which can be imperative for proper function. However, cells frequently experience unexpected environmental perturbations that might induce phenotypic switching. How cells maintain phenotypic states in the face of environmental fluctuations remains an open question. Here, we use environmental perturbations to characterize the resilience of phenotypic states in a synthetic gene network near a critical transition. We find that far from the critical transition an environmental perturbation may induce little to no phenotypic switching, whereas close to the critical transition the same perturbation can cause many cells to switch phenotypic states. This loss of resilience was observed for perturbations that interact directly with the gene circuit as well as for a variety of generic perturbations-such as salt, ethanol, or temperature shocks-that alter the state of the cell more broadly. We obtain qualitatively similar findings in natural gene circuits, such as the yeast GAL network. Our findings illustrate how phenotypic memory can become destabilized by environmental variability near a critical transition.

No MeSH data available.


Related in: MedlinePlus