Fig 1.
Autotrophic and heterotrophic CO2 fixation.
a) Example of a typical autotrophic CO2 assimilation cycle (e.g. the Calvin-Benson-Bassham or reductive tricarboxylic acid cycle). ATP and reduction equivalents are provided by photo- or chemosynthesis. b) Heterotrophic CO2 assimilation can occur via linear pathways from a carbon substrate to certain products. If needed, ATP and/or reduction equivalents are generated from the substrate itself. Depending on the particular substrate-product combination, different amounts of CO2 can be assimilated.
Table 1.
CO2 and capturing reactions in the genome-scale model iJO1366.
The last column indicates which of these reactions are contained in ECC2.
Table 2.
Maximal CO2 assimilation yields and thermodynamic properties for the top 15 products in the core model ECC2 with glucose or glycerol as substrate.
#C-atoms: number of carbon atoms per product.: maximal yield of fixed CO2 per mol substrate consumed;
: maximal (carbon-normalized) CO2 assimilation yield;
: maximal product yield (corresponding optimal MDF in parentheses).
: maximal product yield if a minimal MDF of 3.0 is demanded (minimal pathway length with MDF ≥ 3.0 in parentheses). MDFmax (
): maximal MDF (corresponding maximal CO2 assimilation yield in parentheses).
Table 3.
Maximal CO2 assimilation yields and thermodynamic properties for the top 15 products in the genome-scale model iJO1366 with glucose or glycerol as substrate.
#C-atoms: number carbon atoms per product.: maximal yield of fixed CO2 per mol substrate;
: maximal (carbon-normalized) CO2 assimilation yield;
: maximal product yield (corresponding maximal MDF in parentheses).
at MDF ≥ 3.0: maximal product yield if a minimal MDF of 3.0 is demanded (minimal pathway length with MDF ≥ 3.0 in parentheses). MDFmax (
): maximal MDF (with maximal CO2 assimilation yield in parentheses).
Table 4.
Number of products with net CO2 fixation for which a carboxylation reaction is essential and number of products requiring one or two essential carboxylation reactions.
Table 5.
Number of products in the ECC2 and iJO1366 model with thermodynamically feasible net CO2 assimilation with glucose and glycerol as substrate.
For each model and substrate, the number of stoichiometrically and thermodynamically feasible substrate-product combinations with net CO2 fixation is given and compared with the number of all stoichiometrically feasible substrate-product combinations (in parentheses: relative proportion of thermodynamically feasible substrate-product combinations).
Fig 2.
MDF and CO2 assimilation yield of EMs for selected substrate-product combinations.
EMs with the same color share the same MDF. The black solid line indicates the optimal MDF for a given CO2 assimilation yield.
Fig 3.
Optimal MDF depending on CO2 assimilation yield for selected substrate-product combinations in the genome-scale model iJO1366.
Fig 4.
Robustness of thermodynamic feasibility of CO2 net fixation with respect to varying pH values.
(a) Number of thermodynamically feasible products in iJO1366 with CO2 net assimilation. (b) Average maximal MDF for their synthesis. Black lines and diamonds: substrate glycerol; red line: substrate glucose.