Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium
Summary (2 min read)
Model reconstruction.
- Experimentally measured concentrations of biomass components are available for R. palustris when grown on acetate 13 , and were used to develop the biomass equation (see Supplementary File 1).
- To minimize the addition of low-confidence reactions during gap-filling, the process was broken down into two steps.
- At the end of this step, the majority of the gaps in the network that precluded the production of biomass existed in partially incomplete linear pathways.
- Finally, annotated R. palustris genes were mined from three databases (KEGG 34 , BioCyc 35 , and UniProt 36 ) to validate the Gene-Protein-Reaction (GPR) associations established in the model and to include GPR relationships for reactions added during the gap-filling process (see Supplementary File 3).
Model simulations.
- Parsimonious Flux Balance Analysis (pFBA) 37 was used to simulate growth under different environmental conditions.
- PFBA is analogous to FBA but adds a second objective that minimizes the sum of all reaction fluxes.
- The two objectives were reformulated into one function through objective tilting 38 as displayed below.
Maximize v v subject to S v i I
- Parameters LB j and UB j denote the minimum and maximum allowable fluxes for reaction j, respectively.
- V biomass is the flux of the biomass reaction which mimics the cellular growth rate.
Model validation.
- Model accuracy for each growth condition was calculated by taking the sum of percent errors between pFBA-predicted and MFA values (see Supplementary File 4 for an example).
- In addition, R. palustris' essential genes, determined experimentally for aerobic growth on acetate 31 , were used to validate the essential genes predicted by the model.
- If a reaction knockout resulted in a predicted growth rate that was less than 10% of the wild type growth rate, the reaction was considered essential 41, 42 .
- Reaction GPRs were then used to map the list of essential reactions to essential genes.
- Finally, the list of experimentally determined essential metabolic genes 31 were compared with model predicted essential genes to determine the specificity and sensitivity of the predictions (see Supplementary File 5).
Results and Discussion
- Overall, the 940 genes associated with 1393 model reactions account for 62% of the genes involved in energy metabolism, biosynthesis, carbon & nitrogen metabolism, and cellular processes in R. palustris' genome 3 .
- PFBA avoids these false predictions by the additional constraint that reaction fluxes should be minimized.
- In silico gene essentiality analysis identified 368 essential reactions, out of which 249 were associated with gene annotations in the model.
- Moreover, the rates of quinol oxidation and quinone reduction were equivalent, indicating that the quinone pool was more reduced when compared to the redox state during growth on acetate and butyrate.
- In the LL region, growth was highly dependent on the amount of light available and the model predicted that all of the ATP produced was used to convert the carbon source into biomass precursors.
conclusion
- A genome-scale metabolic network (iRpa940) was used to propose a system-wide mechanistic model of the interactive system that includes photosynthesis, carbon dioxide fixation, and the quinone redox state.
- The model was validated using experimental genome essentiality data 31 (84% accuracy) and flux measurement data 13, 14 for four carbon sources (5-19% prediction error).
- Model simulations predicted the presence of an unidentified quinol sink.
- Predictions also indicated that the extent of CO 2 fixation is dependent on the amount of ATP present, with the quinone redox state acting as a feed-forward signal to the CBB system.
- Going forward, the proposed mechanism can be used to generate strategies for engineering strains capable of more efficiently harnessing photosynthetic energy, and that have the ability to reroute energy towards bio-production and lignin valorization.
Did you find this useful? Give us your feedback
Citations
16 citations
8 citations
1 citations
References
24,024 citations
3,229 citations
2,973 citations
1,574 citations
1,517 citations
Related Papers (5)
Frequently Asked Questions (17)
Q2. What have the authors stated for future works in "Modeling the interplay between photosynthesis, co2 fixation, and the quinone pool in a purple non- sulfur bacterium" ?
Future experimental work will be conducted to measure the electron transport rate, intracellular ATP concentration, and RuBisCO gene expression across different quinone redox states to strengthen the proposed hypothesis and further refine the model.
Q3. What is the effect of the redox state on the CBB system?
Predictions also indicated that the extent of CO2 fixation is dependent on the amount of ATP present, with the quinone redox state acting as a feed-forward signal to the CBB system.
Q4. What was the effect of the quinols on growth?
During initial phototrophic growth simulations, growth on any of the four carbon sources (acetate, fumarate, succinate, and butyrate) was observed to be hindered due to the accumulation of excess quinols formed in the TCA cycle.
Q5. What is the role of the ribulose carboxylase/oxygenase?
CO2-fixation using the enzyme ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO), nitrogen-fixation through the enzyme nitrogenase12, and supplementation with an electron acceptor (e.g., trimethylamine-N-oxide (TMAO))15 all prevent the inhibitory accumulation of excess reducing agents.
Q6. What is the effect of the light uptake rate on the quinol sink?
Although the model predicted that the rate of CO2 fixation increased linearly with light uptake rate, kinetic and thermodynamic constrains on the highly inefficient CO2-fixing RuBisCO enzyme50 hinders this process at high light uptake.
Q7. Who provided funding to support this work?
Funding to support this work was provided by University of Nebraska-Lincoln Faculty Startup Grant and Nebraska Center for Energy Sciences Research (NCESR) to Rajib Saha.
Q8. What is the redox state of the quinone oxidoreductas?
In this study, a genome-scale metabolic network (iRpa940) was used to propose a system-wide mechanistic model of the interactive system that includes photosynthesis, carbon dioxide fixation, and the quinone redox state.
Q9. What was used to fill the gaps in the network?
the ModelSEED database33 was used to fill the gaps in the network, and a biomass producing model was generated in KBase32.
Q10. How many reactions were annotated during the gap-filling procedure?
Out of the 478 reactions added during gap-filling, 368 were annotated using information from organism-specific databases (see Methods).
Q11. What is the role of the Calvin-Benson-Bassham cycle?
Several studies conducted on R. palustris showed that in addition to the Calvin-Benson-Bassham (CBB) cycle’s role of carbon assimilation during autotrophic growth, the pathway plays a major role in maintaining redox balance under heterotrophic conditions10,12–14.
Q12. What is the redox state of the quinone pool?
Based on this analysis, it is hypothesized that the quinone redox state acts as a feed-forward controller of the CBB pathway, signaling the amount of ATP available.
Q13. What is the function of the quinone redox state?
the quinone redox state is predicted to act as a feed-forward controller to the energetically expensive CBB pathway, indicating how much ATP is available at a given condition.
Q14. What is the effect of the quinol sink on cellular growth?
After the model indicated the presence of an unidentified quinol sink, in silico simulations were combined with published in vivo flux measurements13,14 to study the effect (and the extent) of the quinone redox state on cellular growth, electron transport rate, and CO2 fixation.
Q15. What was the rate of quinone reduction in the TCA cycle?
The quinol sink reaction was treated as a parameter in the model and pFBA simulations were conducted at varying quinol oxidation (sink) rates to determine how light uptake (i.e. Electron Transport Rate or ETR), growth, and CO2 fixation are affected by changes in the quinone redox state (Fig. 2).
Q16. What was the rate of quinol oxidization in the reaction center?
Flux analysis of the electron transport chain (ETC) revealed that the rate of quinol oxidization through the cytochrome bc1 complex was equivalent to the rate of quinone reduction in the Reaction center (RC).
Q17. What is the role of redox state in the ATP cycle?
These results suggest that redox state acts as a feed-forward controller of the highly energy-demanding CBB cycle by regulating the rate of light-generated ATP.