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Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis.

  • Marcel H N Hoefnagel
  • Marjo J C Starrenburg
  • Dirk E Martens
  • Jeroen Hugenholtz
  • Michiel Kleerebezem
  • Iris I Van Swam
  • Roger Bongers
  • Hans V Westerhoff
  • Jacky L Snoep
Microbiology (Reading, Engl.) 2002; 148 : 1003-1013
Abstract
Everyone who has ever tried to radically change metabolic fluxes knows that it is often harder to determine which enzymes have to be modified than it is to actually implement these changes. In the more traditional genetic engineering approaches 'bottle-necks' are pinpointed using qualitative, intuitive approaches, but the alleviation of suspected 'rate-limiting' steps has not often been successful. Here the authors demonstrate that a model of pyruvate distribution in Lactococcus lactis based on enzyme kinetics in combination with metabolic control analysis clearly indicates the key control points in the flux to acetoin and diacetyl, important flavour compounds. The model presented here (available at http://jjj.biochem.sun.ac.za/wcfs.html) showed that the enzymes with the greatest effect on this flux resided outside the acetolactate synthase branch itself. Experiments confirmed the predictions of the model, i.e. knocking out lactate dehydrogenase and overexpressing NADH oxidase increased the flux through the acetolactate synthase branch from 0 to 75% of measured product formation rates.

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
AC 0.01 default_compartment
ACAL 0.11 default_compartment
ACCOA 0.11 default_compartment
ACET 0.00001 default_compartment
ACETOUT 0.001 default_compartment
ACLAC 0.00001 default_compartment
ACP 0.03145 default_compartment
ADP 4.9 default_compartment
ATP 0.1 default_compartment
BUT 0.01 default_compartment
COA 0.89 default_compartment
ETOH 0.1 default_compartment
GLC 15.0 default_compartment
LAC 0.1 default_compartment
NAD 6.33 default_compartment
NADH 3.67 default_compartment
O2 0.2 default_compartment
P 10.0 default_compartment
PYR 1.0 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 GLC + {2.0}NAD + {2.0}ADP = {2.0}PYR + {2.0}NADH + {2.0}ATP

(Vmax1*(GLC/Km1GLC)*(NAD/Km1NAD)*(ADP/Km1ADP))/((1+GLC/Km1GLC+PYR/Km1PYR)*(1+NAD/Km1NAD+NADH/Km1NADH)*(1+ADP/Km1ADP+ATP/Km1ATP))
v_10 ACCOA + P = ACP + COA

((Vmax10/(Ki10ACCOA*Km10P))*(ACCOA*P-((ACP*COA)/(Keq10))))/(1+(ACCOA/Ki10ACCOA)+(P/Ki10P)+(ACP/Ki10ACP)+(COA/Ki10COA)+((ACCOA*P)/(Ki10ACCOA*Km10P))+((ACP*COA)/(Km10ACP*Ki10COA)))
v_11 ACP + ADP = AC + ATP

(Vmax11*(ACP/Km11ACP)*(ADP/Km11ADP)*(1-((AC*ATP)/(ACP*ADP*Keq11))))/((1+(ACP/Km11ACP)+(AC/Km11AC))*(1+(ADP/Km11ADP)+(ATP/Km11ATP)))
v_12 PYR + NAD + COA = NADH + ACCOA

Vmax12*((PYR/Km12PYR)*(NAD/Km12NAD)*(COA/Km12COA)/((1+(PYR/Km12PYR))*(1+(NAD/Km12NAD)+(NADH/Km12NADH))*(1+(COA/Km12COA)+(ACCOA/Km12ACCOA))))*(1/(1+((Ki12*NADH)/NAD)))
v_13 NADH + ACCOA = NAD + COA + ACAL

(Vmax13*(NADH*ACCOA)/(Km13NADH*Km13ACCOA)-(Vmax13*NAD*COA*ACAL)/(Km13NADH*Km13ACCOA*Keq13))/((1+NADH/Km13NADH+NAD/Km13NAD)*(1+ACCOA/Km13ACCOA+COA/Km13COA)* (1+ACAL/Km13ACAL))
v_14 ACAL + NADH = ETOH + NAD

(Vmax14*(ACAL/Km14ACAL)*(NADH/Km14NADH)*(1-((ETOH*NAD)/(ACAL*NADH*Keq14))))/((1+(ACAL/Km14ACAL)+(ETOH/Km14ETOH))*(1+(NADH/Km14NADH)+(NAD/Km14NAD)))
v_2 PYR + NADH = LAC + NAD

(Vmax2*(PYR/Km2PYR)*(NADH/Km2NADH)*(1-((LAC*NAD)/(PYR*NADH*Keq2))))/((1+(PYR/Km2PYR)+(LAC/Km2LAC))*(1+(NADH/Km2NADH)+(NAD/Km2NAD)))
v_3 ATP = ADP + P

Vmax3*((ATP/ADP)^n3)/((KATP^n3 + ((ATP/ADP)^n3)))
v_4 NADH + O2 = NAD

(Vmax4*NADH/Km4NADH*O2/Km4O)/((1+NADH/Km4NADH+NAD/Km4NAD)*(1+O2/Km4O))
v_5 {2.0}PYR = ACLAC

Vmax5*(PYR/Km5PYR)*(1-(ACLAC/(PYR*Keq5)))*(((PYR/Km5PYR)+(ACLAC/Km5ACLAC))^(h5-1))/(1+(((PYR/Km5PYR)+(ACLAC/Km5ACLAC))^h5))
v_6 ACLAC = ACET

(Vmax6*ACLAC/Km6ACLAC)/(1 + ACLAC/Km6ACLAC + ACET/Km6ACET)
v_7 ACET = ACETOUT

Vmax7*ACET/(Km7ACET + ACET)
v_8 ACLAC = ACET

k8*ACLAC
v_9 ACET + NADH = BUT + NAD

(Vmax9*(ACET/Km9ACET)*(NADH/Km9NADH)*(1-((BUT*NAD)/(ACET*NADH*Keq9))))/((1+(ACET/Km9ACET)+(BUT/Km9BUT))*(1+(NADH/Km9NADH)+(NAD/Km9NAD)))

Global parameters

Id Value
KATP 6.196
Keq10 0.0065
Keq11 174.217
Keq13 1.0
Keq14 12354.9
Keq2 21120.69
Keq5 9000000000000.0
Keq9 1400.0
Ki10ACCOA 0.2
Ki10ACP 0.2
Ki10COA 0.029
Ki10P 2.6
Ki12 46.4159
Km10ACP 0.7
Km10P 2.6
Km11AC 7.0
Km11ACP 0.16
Km11ADP 0.5
Km11ATP 0.07
Km12ACCOA 0.008
Km12COA 0.014
Km12NAD 0.4
Km12NADH 0.1
Km12PYR 1.0
Km13ACAL 10.0
Km13ACCOA 0.007
Km13COA 0.008
Km13NAD 0.08
Km13NADH 0.025
Km14ACAL 0.03
Km14ETOH 1.0
Km14NAD 0.08
Km14NADH 0.05
Km1ADP 0.04699
Km1ATP 0.01867
Km1GLC 0.1
Km1NAD 0.1412
Km1NADH 0.08999
Km1PYR 2.5
Km2LAC 100.0
Km2NAD 2.4
Km2NADH 0.08
Km2PYR 1.5
Km4NAD 1.0
Km4NADH 0.041
Km4O 0.2
Km5ACLAC 100.0
Km5PYR 50.0
Km6ACET 100.0
Km6ACLAC 10.0
Km7ACET 5.0
Km9ACET 0.06
Km9BUT 2.6
Km9NAD 0.16
Km9NADH 0.02
Vmax1 2397.0
Vmax10 42.0
Vmax11 2700.0
Vmax12 259.0
Vmax13 97.0
Vmax14 162.0
Vmax2 5118.0
Vmax3 900.0
Vmax4 118.0
Vmax5 600.0
Vmax6 106.0
Vmax7 200.0
Vmax9 105.0
h5 2.4
k8 0.0003
n3 2.58

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments