What is Metabolic Flux Analysis?

1
What is Metabolic Flux Analysis?

• Starts with the metabolic network
• Assumes steady-state behavior
• Constrain with Thermodynamics
• Add Nutrient conditions
• Choose an objective Biomass growth
• Predicts growth rate for mutant and wild-type
  organisms under different conditions.

2
Start with the metabolic network
3
Stoichiometric Matrix Representation of the
metabolic network
R1 R2 R3 R4 R5 R6 R7 R8 R8
A 1 -1 -1
B 1 -1 -2
C 1 1 -1
D 2 1 -1
E -1 1
F 1 -1
R1 A_ext ? A R2 A ? B R3 A ? C
R4 B E ? 2D
R5 E_ext? E R6 2B ? C F R7 C ? D R8 D
?D_ext R9 F ?F_ext
4
What is a metabolic flux?
Source fluxes
Metabolite Pool
Sink fluxes
5
What is a metabolic flux?
For a reaction of stoichiometry R2 A ? B the
rate of reaction, or flux is equal to
For a reaction of stoichiometry R4 BE ?
2D the flux is equal to
6
What is a metabolic flux?
For a reaction of stoichiometry R4 BE ?
2D The rate of reaction, or flux, is equal to
7
At steady-state, nonlinear dynamics simplify to
linear fluxes.
B
B
k2
v2
P2
k1
v1
A
P1
Aext
A
Aext
k3
P3
v3
C
C
8
At steady-state, the sum of the fluxes that
produce a metabolite is equal to the sum of the
fluxes that consume it.
B
v2
v1
A
Aext
v3
C
9
Stoichiometric Matrix more unknowns than
equations
R1 R2 R4 R4 R5 R6 R7 R8 R9
A 1 -1 -1
B 1 -1 -2
C 1 1 -1
D 2 1 -1
E -1 1
F 1 -1
v1
v2
v3
v4
v5
v6
v7
v8
v9
10
How to determine the metabolic capabilities of a
network?
Uptake v5
E
B
v4
v2
2B
Biomass v8
2D
Uptake v1
A
v6
D
v3
F
v7
C
Waste v9
11
Using Elementary modes to study the steady
state-behavior
v5
v5
E
E
B
E
E
B
v4
v2
2B
v4
v2
2B
2D
v1
2D
A
v1
v6
v8
A
D
v8
v6
D
v3
v3
F
v7
F
C
v7
C
R9
v9
v5
V1 v2 v3 v4 v5 v6 v7 v8 v9
A 1 -1 -1
B 1 -1 -2
C 1 1 -1
D 2 1 -1
E -1 1
F 1 -1
E
B
v4
v2
2B
2D
v1
A
v8
v6
D
v3
F
v7
C
v9
12
How to make predictions about the behavior of the
metabolic network?
Uptake v5
E
B
v4
v2
2B
Biomass v8
2D
Uptake v1
A
v6
D
v3
F
v7
C
Waste v9
13
Optimal wild-type flux distribution
v5
10
Optimal Growth Flux
E
B
v4
2B
v2
10
10
2D
v1
v8
A
v6
10
D
20
v3
F
v7
C
v9
14
Optimal mutant flux distribution
v5
E
B
v4
2B
v2
STOP
2D
v1
v8
A
v6
10
D
10
v3
10
10
F
C
v7
v9
15
Suboptimal mutant flux distribution
v5
E
B
v4
2B
v2
STOP
6.7
2D
v1
v8
3.3
A
10
v6
D
6.7
v3
3.3
6.7
F
C
v7
3.3
v9