Info! This is a derivative of the model smallbone11
Info! This is a derivative of the model levchenko1

snoep2

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Control of specific growth rate in Saccharomyces cerevisiae.

  • Jacky L Snoep
  • M Mrwebi
  • JM Schuurmans
  • Johann M Rohwer
  • MJ Teixeira de Mattos
Microbiology (Reading, Engl.) 2009; 155 : 1699-1707
Abstract
In this contribution we resolve the long-standing dispute whether or not the Monod constant (K(S)), describing the overall affinity of an organism for its growth-limiting substrate, can be related to the affinity of the transporter for that substrate (K(M)). We show how this can be done via the control of the transporter on the specific growth rate; they are identical if the transport step has full control. The analysis leads to the counter-intuitive result that the affinity of an organism for its substrate is expected to be higher than the affinity of the enzyme that facilitates its transport. Experimentally, we show this indeed to be the case for the yeast Saccharomyces cerevisiae, for which we determined a K(M) value for glucose more than two times higher than the K(S) value in glucose-limited chemostat cultures. Moreover, we calculated that at glucose concentrations of 0.03 and 0.29 mM, the transport step controls the specific growth rate at 78 and 49 %, respectively.

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
Id Name Spatial dimensions Size
default_compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
Biom 0.03 default_compartment
Sext 0.0 default_compartment
Sint 0.0 default_compartment
Sr 20.0 default_compartment
Xint 0.0 default_compartment
p 0.0 default_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
v_1 Sr = Sext

Dil*Sr
v_2 v_2 Sext = Sint

Biom*(Vm2/K2S*(Sext - Sint/(0.0001*Keq2)) / (1 + Sext/K2S + Sint/(0.0001*K2Sin)))
v_3 Sext = p

Dil*Sext
v_4 v_4 Sint = Xint

Biom*(Vm4/K4Sint*(Sint/(0.0001) - Xint/(0.0001*Keq4)) / (1 + Sint/(0.0001*K4Sint) + Xint/(0.0001*K4X)))
v_5 Xint = Biom

Biom*(Vm5*Xint/(0.0001*K5X)/(1+Xint/(0.0001*K5X)))
v_6 Biom = p

Dil*Biom

Global parameters

Id Value
Dil 0.1
K2S 0.9
K2Sin 0.9
K4Sint 1.0
K4X 1.0
K5X 2.0
Keq2 1.0
Keq4 100.0
Vm2 9.0
Vm4 10.0
Vm5 0.52

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments