Analysis and Optimization of C3 Photosynthetic Carbon Metabolism

Abstract

Abstract-We have studied the C3 photosynthetic carbon metabolism centering our investigation on the following four design principles. (1) Optimization of the photosynthetic rate by modifying the partitioning of resources between the different enzymes of the C3 photosynthetic carbon metabolism using a constant amount of protein-nitrogen. (2) Identify sensitive and less sensitive enzymes of the studied model. (3) Maximize photosynthetic productivity rate through the choice of robust enzyme concentrations using a new precise definition of robustness. (4) Modeling photosynthetic carbon metabolism as a multiobjective problem of two competing biological selection pressures: light-saturated photosynthetic rate versus total protein-nitrogen requirement. Using the designed single-objective optimization algorithms, PAO and A-CMA-ES, we have obtained an increase in photosynthetic productivity of the 135% from 15.486 µmol m −2 s −1 to 36.382 µmol m −2 s −1 , and improving the previous best-found photosynthetic productivity value (27.261 µmol m −2 s −1 , 76% of enhancement). Optimized enzyme concentrations express a maximal local robustness (100%) and a high global robustness (97.2%), satisfactory properties for a possible "in vitro" manufacturing of the optimized pathway. Morris sensitivity analysis shows that 11 enzymes over 23 are high sensitive enzymes, i.e., the most influential enzymes of the carbon metabolism model. Finally, we have obtained the tradeoff between the maximization of the leaf CO2 uptake rate and the minimization of the total protein-nitrogen concentration. This trade-off search has been carried out for the three c i concentrations referring to the estimate of CO2 concentration in the atmosphere characteristic of 25 million years ago, nowadays and in 2100 a.C. Remarkably, the three Pareto frontiers identify the highest photosynthetic productivity rates together with the fewest protein-nitrogen usage.

Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism

“…The aim of this is evidently the evaluation of the contribution of these sensitive enzymes in the optimization of the photosynthetic metabolism considered. [2] to let a pool of solutions evolve in an archipelago fashion. Fixing at their natural value all but sensitive enzymes, PAO has evaluated a number of new enzyme concentration profiles and has associated a CO 2 Uptake to each one of them by computing the system of ODEs mentioned above.…”

“…This value is within the range of typical CO 2 Uptake rates calculated in the field for C 3 leaves [5] and can then be considered a good approximation. More recently, new efficient models showed that strategies modifying enzyme concentrations may lead to an increase in CO 2 amount of 135% with respect to the initial natural value [2,3]. In particular, Stracquadanio et al [2] used also the concepts of robustness and sensitivity for assessing the evaluation of confidence limits in the results obtained by perturbing the new identified solutions; this simulates typical "in-vitro" implementation variables (refer to Sensitivity and Robustness in Sect.…”

“…In this paper, we improve and advance the work started in [2] by defining and exploiting an investigation pipe-line that composes Sensitivity Analysis (SA), Single-and Multi-objective optimization, and Robustness Analysis (RA) to move toward the study of the artificial photosynthesis. More in detail, these techniques are composed into the following pipe-line: beginning with a (1) system of ODEs (refer to coming paragraph) to have a computational model of C 3 photosynthetic pathway, (2) we exploit SA to identify which are the sensitive tuning gears of the system, then (3) we exploit SO and MO optimization to re-optimize the pathway in a functional fashion; (4) we adopt RA to have a quantitative prediction about the stability of the lately found optimizations.…”

“…In particular, Stracquadanio et al [2] used also the concepts of robustness and sensitivity for assessing the evaluation of confidence limits in the results obtained by perturbing the new identified solutions; this simulates typical "in-vitro" implementation variables (refer to Sensitivity and Robustness in Sect. 2). An important question regarding this re-optimization is: why did the evolution process and not optimize enzyme concentration in order to maximize CO 2 fixation?…”

“…The modeling of this pathway (and allied pathway in Carbon metabolism plants) aims at optimization with respect to some specific functional targets of interest for possible biotechnological applications. Photosynthesis models showed that modifying enzyme concentration would allow the increase of the C 3 -cycle efficiency, while maintaining the total amount of Nitrogen constant in the plant [1][2][3]. Where the biochemical pathway of the Calvin cycle is concerned, a seminal work by Zhu et al [1], based on the Farquhar model [4], showed, with the help of an evolutionary algorithm, how enzyme concentration rearrangements could be capable of increasing the total amount of CO 2 Uptake by a factor of 76% with respect to the results obtained with the initial concentrations characteristic of the natural leaf.…”