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Efficient Behavior of Photosynthetic Organelles via Pareto Optimality, Identifiability, and Sensitivity Analysis

Carapezza, Giovanni and Umeton, Renato and Costanza, Jole and Angione, Claudio and Stracquadanio, Giovanni and Papini, Alessio and Lió, Pietro and Nicosia, Giuseppe (2013) 'Efficient Behavior of Photosynthetic Organelles via Pareto Optimality, Identifiability, and Sensitivity Analysis.' ACS Synthetic Biology, 2 (5). pp. 274-288. ISSN 2161-5063

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In this work, we develop methodologies for analyzing and cross comparing metabolic models. We investigate three important metabolic networks to discuss the complexity of biological organization of organisms, modeling, and system properties. In particular, we analyze these metabolic networks because of their biotechnological and basic science importance: the photosynthetic carbon metabolism in a general leaf, the Rhodobacter spheroides bacterium, and the Chlamydomonas reinhardtii alga. We adopt single- and multi-objective optimization algorithms to maximize the CO2 uptake rate and the production of metabolites of industrial interest or for ecological purposes. We focus both on the level of genes (e.g., finding genetic manipulations to increase the production of one or more metabolites) and on finding concentration enzymes for improving the CO2 consumption. We find that R. spheroides is able to absorb an amount of CO2 until 57.452 mmol h-1 gDW-1, while C. reinhardtii obtains a maximum of 6.7331. We report that the Pareto front analysis proves extremely useful to compare different organisms, as well as providing the possibility to investigate them with the same framework. By using the sensitivity and robustness analysis, our framework identifies the most sensitive and fragile components of the biological systems we take into account, allowing us to compare their models. We adopt the identifiability analysis to detect functional relations among enzymes; we observe that RuBisCO, GAPDH, and FBPase belong to the same functional group, as suggested also by the sensitivity analysis. © 2012 American Chemical Society.

Item Type: Article
Uncontrolled Keywords: metabolic CAD; synthetic biology; multi-objective optimization; sensitivity analysis; robustness analysis; photosynthetic yield
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions: Faculty of Science and Health
Faculty of Science and Health > Computer Science and Electronic Engineering, School of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 07 Feb 2017 12:39
Last Modified: 06 Jan 2022 14:43

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