vanHeerden2

This model reproduces Figure 4C and Figure 4D of the paper.

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Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells.

  • Johan H van Heerden
  • Meike T Wortel
  • Frank J Bruggeman
  • Joseph J Heijnen
  • Yves J M Bollen
  • Robert Planqué
  • Josephus Hulshof
  • Tom G O'Toole
  • S Aljoscha Wahl
  • Bas Teusink
Science 2014; 343 (6174): 1245114
Abstract
Cells need to adapt to dynamic environments. Yeast that fail to cope with dynamic changes in the abundance of glucose can undergo growth arrest. We show that this failure is caused by imbalanced reactions in glycolysis, the essential pathway in energy metabolism in most organisms. The imbalance arises largely from the fundamental design of glycolysis, making this state of glycolysis a generic risk. Cells with unbalanced glycolysis coexisted with vital cells. Spontaneous, nongenetic metabolic variability among individual cells determines which state is reached and, consequently, which cells survive. Transient ATP (adenosine 5'-triphosphate) hydrolysis through futile cycling reduces the probability of reaching the imbalanced state. Our results reveal dynamic behavior of glycolysis and indicate that cell fate can be determined by heterogeneity purely at the metabolic level.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
1.0 litre
1.0 metre
1.0 mole
1.0 second
1.0 metre^(2.0)
Id Name Spatial dimensions Size
compartment compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
EtOH EtOH 0.0 compartment (compartment)
Glycerol Glycerol 0.0 compartment (compartment)
PiVac PiVac 0.0 compartment (compartment)
atp atp 1.0 compartment (compartment)
fbp fbp 2.0 compartment (compartment)
g6p g6p 0.0 compartment (compartment)
phos phos 10.0 compartment (compartment)

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
v1 v1 {2.0}atp + g6p = fbp

VMAXPFK * atp / (KMPFKATP + atp * (1 + atp / KiPFKATP))
v2 v2 {2.0}phos + fbp = {4.0}atp + {2.0}EtOH

VMAXLG * (fbp / (KMLGF16P + fbp)) * ((atot - atp) / KMLGADP) * (phos / KMLGP) / ((1 + (atot - atp) / KMLGADP) * (1 + phos / KMLGP))
v3 v3 atp = phos

KATPASE * atp
v4 v4 PiVac = phos

k6 * (pT - phos)
v5 v5 fbp = Glycerol + {2.0}phos

VMAXGLYC * (fbp / (KMLGF16P + fbp))

Global parameters

Id Value
KATPASE 10.0
KMLGADP 0.1
KMLGF16P 1.0
KMLGP 2.0
KMPFKATP 0.1
KiPFKATP 3.0
VMAXGLYC 0.0
VMAXLG 10.0
VMAXPFK 10.0
atot 5.0
k6 0.3
pT 10.0

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments