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. 2012 Jul 9;7(7):e39396. doi: 10.1371/journal.pone.0039396

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Nikerel et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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In each plot, the dots (•) describe the sampled enzyme levels relative to reference state, colored according to the feasibility criteria specified in each plot above the color legend bar; the squares (▪) are the experimental data either from [41] or [43], white being the “wild-type” (10th generation) and black being the “evolved strain” (200th generation) and the arrow indicates the direction of the number of generations during the experiment (time). Enzymes not shown change only 10% from their reference state. fig:LongChemostatPGI-ALD: The function feasibility in terms of PGI and ALD, the color corresponds the total cost of the enzymes (). The experimental data from [43] shows that the cells evolved to an economized state.fig:LongChemostatGLT-HK: Function feasibility inspected for glucose transporter (GLT) and hexokinase (HK). The colouring is similar to fig:LongChemostatPGI-ALD, the sum of enzyme levels. The hypothesis on enzyme economy fails to predict the levels of these two enzymes for the evolved strain. fig:LongChemostatPGI-GLT: The evolution of glucose transporter and PGI enzymes inspected via homeostasis feasibility, as the co-response of extracellular glucose and uptake rate (). Cells evolve to a state where they are more apt to use extracellular resources. fig:LongChemostatPGI-ALD-ATP: The evolved state is predicted to allow yeast to respond quicker to external perturbations, as indicated by ATP temporal responsiveness feasibility as the color code for PGI and ALD. The experimental verification of this prediction is presented in fig:LongChemostatATPpulse where the response of ATP to a glucose perturbation (taken from [41]) is presented. The y-axis is the ATP level relative to the state before perturbation and x-axis represent the time in seconds. Evolved cells (•) respond quicker to glucose perturbation, when compared to wild-type cells (♦). fig:LongChemostatPGI-PFK: the function feasibility inspected for PFK and PGI. PFK levels, being already at the edge of the feasible space, can not further be decreased.

Inline graphic — In each plot, the dots (•) describe the sampled enzyme levels relative to reference state, colored according to the feasibility criteria specified in each plot above the color legend bar; the squares (▪) are the experimental data either from [41] or [43], white being the “wild-type” (10th generation) and black being the “evolved strain” (200th generation) and the arrow indicates the direction of the number of generations during the experiment (time). Enzymes not shown change only 10% from their reference state. fig:LongChemostatPGI-ALD: The function feasibility in terms of PGI and ALD, the color corresponds the total cost of the enzymes (). The experimental data from [43] shows that the cells evolved to an economized state.fig:LongChemostatGLT-HK: Function feasibility inspected for glucose transporter (GLT) and hexokinase (HK). The colouring is similar to fig:LongChemostatPGI-ALD, the sum of enzyme levels. The hypothesis on enzyme economy fails to predict the levels of these two enzymes for the evolved strain. fig:LongChemostatPGI-GLT: The evolution of glucose transporter and PGI enzymes inspected via homeostasis feasibility, as the co-response of extracellular glucose and uptake rate (). Cells evolve to a state where they are more apt to use extracellular resources. fig:LongChemostatPGI-ALD-ATP: The evolved state is predicted to allow yeast to respond quicker to external perturbations, as indicated by ATP temporal responsiveness feasibility as the color code for PGI and ALD. The experimental verification of this prediction is presented in fig:LongChemostatATPpulse where the response of ATP to a glucose perturbation (taken from [41]) is presented. The y-axis is the ATP level relative to the state before perturbation and x-axis represent the time in seconds. Evolved cells (•) respond quicker to glucose perturbation, when compared to wild-type cells (♦). fig:LongChemostatPGI-PFK: the function feasibility inspected for PFK and PGI. PFK levels, being already at the edge of the feasible space, can not further be decreased.