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Clark et al. 2014

Ryan L. Clark et al., Insights into the industrial growth of cyanobacteria from a model of the carbon-concentrating mechanism, AIChE Journal, 2014

The direct production of fuels and chemicals from CO2 using genetically engineered photosynthetic cyanobacteria would bypass much of the land, water, and transportation problems associated with biomass cultivation for traditional fermentation or catalytic conversion. However, current productivity of chemicals by these engineered cyanobacteria is too low to be economically feasible. The most troublesome bottleneck in cyanobacterial photosynthesis is the uptake of CO2, the building block from which molecules of interest are synthesized. Therefore, a profitable and controllable industrial process for the production of small molecules by cyanobacteria must be assisted by the development of a platform organism capable of metabolizing a higher flux of CO2 and able to efficiently convert that flux into desired chemicals. Modeling of cyanobacterial growth on both an intracellular and macroscopic level can be used to understand the mechanisms of CO2-fixation and their implications in a large scale process.

The cyanobacterial carbon dioxide concentrating mechanism (CCM) comprises a system of structural proteins and enzymes that enable cyanobacteria to increase the local concentration of CO2 around the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) by up to three orders of magnitude. This mechanism allows cyanobacterial growth in their native aqueous environment with low concentrations of CO2. A quantitative model of this mechanism is described in this work and shows that the CCM is unnecessary for growth in media in equilibrium with a gas phase of 10% CO2, a concentration readily available in abundant industrial flue gas. Because the proteins involved in the CCM are large, and therefore costly to synthesize, elimination of their production in a high-CO2 environment could provide a significant metabolic benefit to cyanobacteria. Integrating these results with a macroscopic growth model will improve understanding of cyanobacterial growth on an industrial scale.


model: Clark et al. 2014

Ryan L. Clark et al., Insights into the industrial growth of cyanobacteria from a model of the carbon-concentrating mechanism, AIChE Journal, 2014


publication: Clark et al. 2014
Contains:
Initial expression: 1
Simulation type: fixed
Details
Initial expression: CO2_ext
Simulation type: reaction
Details
Initial expression: (k2/k3)*CO2_cyt*OH_cyt
Simulation type: reaction
Details
Initial expression: 1
Simulation type: fixed
Details
Initial expression: CO2_cyt
Simulation type: reaction
Details
Initial expression: (k2/k3)*CO2_carb*OH_carb
Simulation type: reaction
Details
Function: CO2 Fixation function (irreversible)
Reaction rate: (v2*CO2_carb)/(CO2_carb+K4*(1+O2_carb/K5))
Kinetic rate constant Value
O2_carb 4*10^-4
v2 k7*Nsites/Vcarb
K4 1.9*10^-4
K5 1.3*10^-3
Details
Function: Four constants (irreversible)
Reaction rate: factorCo2dehyd*fast*k2*OH_carb*CO2_carb
Kinetic rate constant Value
OH_carb "kW"/10^(-"pH_carb")
fast 100
k2 12100+1156*(Temperature-25)
factorCo2dehyd 1
Details
Function: light-dependend Mass Action (irreversible)
Reaction rate: k2*CO2_cyt*OH_cyt
Kinetic rate constant Value
OH_cyt "kW"/10^(-"pH_cyt")
k2 12100+1156*(Temperature-25)
Details
Function: CO2transport in function (irreversible)
Reaction rate: fast*(CO2_ext-CO2_cyt)
Kinetic rate constant Value
CO2_ext "kH"*"PCO2"
fast 100
Details
Function: Three constants (irreversible)
Reaction rate: factorHCO3dehyd*fast*k3*HCO3_carb
Kinetic rate constant Value
fast 100
k3 0.00006+0.00006*(Temperature-25)
factorHCO3dehyd 1
Details
Function: Mass Action (irreversible)
Reaction rate: k3*HCO3_cyt
Kinetic rate constant Value
k3 0.00006+0.00006*(Temperature-25)
Details
Function: Henri-Michaelis-Menten in volume (irreversible)
Reaction rate: ((v1*HCO3_ext)/(K1 + HCO3_ext))/Vcell
Kinetic rate constant Value
HCO3_ext ("k2"/"k3")*"CO2_ext"*"OH_ext"
HCO3_ext ("k2"/"k3")*"CO2_ext"*"OH_ext"
K1 2.2*10^-4
v1 2e-18
Vcell 5.2*10^-16
Details
Function: Mass Action (reversible)
Reaction rate: fast*HCO3_cyt-fast*HCO3_carb
Kinetic rate constant Value
fast 100
fast 100
Details

Constant quantities

Initial expression: 2e-18
Simulation type: fixed
Initial expression: 2.2*10^-4
Simulation type: fixed
Initial expression: 1.9*10^-4
Simulation type: fixed
Initial expression: 1.3*10^-3
Simulation type: fixed
Initial expression: 10^-14
Simulation type: fixed
Initial expression: 8.2
Simulation type: fixed
Initial expression: 8
Simulation type: fixed
Initial expression: 8
Simulation type: fixed
Initial expression: 100
Simulation type: fixed
Initial expression: 4*10^-4
Simulation type: fixed
Initial expression: 0.0004
Simulation type: fixed
Initial expression: 38
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 1.9*10^-23
Simulation type: fixed
Initial expression: 13400
Simulation type: fixed
Initial expression: 1.7*10^-17
Simulation type: fixed
Initial expression: 5.2*10^-16
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed

Assigned quantities

Initial expression: k7*Nsites/Vcarb
Simulation type: assignment
Initial expression: 12100+1156*(Temperature-25)
Simulation type: assignment
Initial expression: 0.00006+0.00006*(Temperature-25)
Simulation type: assignment
Initial expression: 10^-(1.5+0.01*(Temperature-25)+0.1*IonicStrength)
Simulation type: assignment
Initial expression: kH*PCO2
Simulation type: assignment
Initial expression: (k2/k3)*CO2_ext*OH_ext
Simulation type: assignment
Initial expression: kW/10^(-pH_cyt)
Simulation type: assignment
Initial expression: kW/10^(-pH_ext)
Simulation type: assignment
Initial expression: kW/10^(-pH_carb)
Simulation type: assignment
Initial expression: 10^-(6.4+0.0001*Temperature^2-0.01*Temperature+1.7*IonicStrength^2-1.9*IonicStrength)
Simulation type: assignment
Initial expression: (v2*CO2_carb)/(CO2_carb+K4*(1+O2_carb/K5))
Simulation type: assignment
Initial expression: k3*HCO3_cyt
Simulation type: assignment
Initial expression: k2*CO2_cyt*OH_cyt
Simulation type: assignment
Initial expression: fast*(CO2_ext-CO2_cyt)
Simulation type: assignment
Initial expression: ((v1*HCO3_ext)/(K1 + HCO3_ext))/Vcell
Simulation type: assignment
Initial expression: factorCo2dehyd*fast*k2*OH_carb*CO2_carb
Simulation type: assignment
Initial expression: factorHCO3dehyd*fast*k3*HCO3_carb
Simulation type: assignment
Initial expression: fast*HCO3_cyt-fast*HCO3_carb
Simulation type: assignment
Initial expression: (v2*CO2_carb)/(CO2_carb+K4*(1+O2_carb/K5))
Simulation type: assignment
Name Value
cyt 1
carb 1
CO2_cyt CO2_ext
HCO3_cyt (k2/k3)*CO2_cyt*OH_cyt
CO2_carb CO2_cyt
HCO3_carb (k2/k3)*CO2_carb*OH_carb

Constant quantities

Name Value
v1 2e-18
K1 2.2*10^-4
K4 1.9*10^-4
K5 1.3*10^-3
kW 10^-14
pH_ext 8.2
pH_cyt 8
pH_carb 8
fast 100
O2_carb 4*10^-4
PCO2 0.0004
Temperature 38
IonicStrength 0.1
k7 1.9*10^-23
Nsites 13400
Vcarb 1.7*10^-17
Vcell 5.2*10^-16
factorCo2dehyd 1
factorHCO3dehyd 1

Assigned quantities

Name Value
v2 k7*Nsites/Vcarb
k2 12100+1156*(Temperature-25)
k3 0.00006+0.00006*(Temperature-25)
kH 10^-(1.5+0.01*(Temperature-25)+0.1*IonicStrength)
CO2_ext kH*PCO2
HCO3_ext (k2/k3)*CO2_ext*OH_ext
OH_cyt kW/10^(-pH_cyt)
OH_ext kW/10^(-pH_ext)
OH_carb kW/10^(-pH_carb)
K6 10^-(6.4+0.0001*Temperature^2-0.01*Temperature+1.7*IonicStrength^2-1.9*IonicStrength)
CO2 fixation rate (v2*CO2_carb)/(CO2_carb+K4*(1+O2_carb/K5))
rate3 k3*HCO3_cyt
rate2 k2*CO2_cyt*OH_cyt
rate6 fast*(CO2_ext-CO2_cyt)
rate1 ((v1*HCO3_ext)/(K1 + HCO3_ext))/Vcell
rate4 factorCo2dehyd*fast*k2*OH_carb*CO2_carb
rate5 factorHCO3dehyd*fast*k3*HCO3_carb
rate7 fast*HCO3_cyt-fast*HCO3_carb
rate8 (v2*CO2_carb)/(CO2_carb+K4*(1+O2_carb/K5))
Name Value
time offset 0  
start time 0  
end time 100  
step 10000  

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