SBML file is attached
We mailed Prof. Costas Maranas from Pennsylvania State University asking if he has an SBML or mat file for the UTEX 2973 model from the paper 'Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient 13C-Labeling Data'. May 16th
His postdoc student John Hendry replied with the SBML file from 'Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973' saying this model was built for the purpose of FBA. He asked us to go through the paper for more details. A copy of the paper is attached here too.
Values for CO2 uptake:
- According to the paper the model is from its 18.377 at optimal conditions
- According to https://doi.org/10.1186/s13068-017-0958-y:
- 12.2 in PBR (3%CO2 and 500 umol/ms^2 photons, 38')- optimal conditions
- 6.7 in shaking flask(atm. CO2, 100 photons, 38', 250 rpm)
Values for photon uptake rate:
Hard to explicitly calculate. Hopefully it isnt a limiting factor compared to CO2. Some methods we can use:
- The actual photon absorption flux of autotrophic C. protothecoides by light-harvesting complexes for metabolic use is difficult because much of the incident light was reflected or scattered before it could generate the light reaction. Here, we applied a simplified approach proposed by Manichaikul et al. (2009) to estimate the photon uptake flux. The conversion rate of incident light to photon absorption flux is assumed to be constant, which is also practicable for the photon saturation point. The minimal light uptake that is sufficient for photosynthetic saturation measured as O2 evolution was calculated to be 37.72 mmol g dry cell weightâˆ’1 hâˆ’1 when autotrophic C. protothecoides grows at its maximal specific growth rate that has ever been reported (Sorokin and Krauss, 1959). The experimental photon flux saturation point was 500 Î¼mol mâˆ’2 sâˆ’1 (Ouyang et al., 2010). Therefore, the actual flux of photon uptake can be estimated with experimentally measured light radiation. (from https://doi.org/10.1104/pp.114.250688)
- We used a dual-optimization strategy to perform simulations of photoautotrophic growth. We set our first objective to maximize the biomass production rate with a net CO2 input of 8.37 mmol/gDW/h (experimentally measured in our lab). Then we set our second objective to minimize the total photon utilization.
It is necessary to put constraints on several reactions to perform accurate simulations of photoautotrophic growth. The maximum net CO2 consumption rate was set to be 8.37 mmol/gDW/h, which was observed at the maximum photoautotrophic growth rate (Fig. 3). There was initially no constraint on total photon input rate (or photosystem I (PSI) or PSII electron transfer rate). Our simulations of growth under photoautotrophic conditions determined that the total photon input rate required to reach maximum growth in the Synechococcus 7002 wild type strain was 99.6 mmol/gDW/h. Thus, 99.6 mmol/gDW/h was set as the maximum photon input rate for all photoautotrophic growth simulations described in this paper. (from https://doi.org/10.1016/j.bbabio.2016.12.007)