Team:Valencia UPV/Modeling/fba

COBRA

The COnstraints Based Reconstruction and Analysis (COBRA) approach to systems biology accepts the fact that we do not possess sufficiently detailed parameter data to precisely model, in the biophysical sense, an organism or plant at the genome scale [1]. The COBRA Toolbox is a freely available Matlab toolbox can be used to perform a variety of COBRA methods, including many FBA-based methods. Models for the COBRA Toolbox are saved in the Systems Biology Markup Language (SBML).

AraGEM Model

AraGEM [2] is the genome-scale metabolic network model covering primary metabolism for a compartmentalized plant cell based on the Arabidopsis (Arabidopsis Thaliana) genome. AraGEM is a comprehensive literature-based model, that accounts for the functions of 1,419 unique open reading frames, 1,748 metabolites, 5,253 gene-enzyme reaction-association entries, and 1,567 unique reactions compartmentalized into the cytoplasm, mitochondrion, plastid, peroxisome, and vacuole. Using efficient resource utilization as the optimality criterion, AraGEM has already been used to predict the classical photorespiratory cycle as well as known key differences between redox metabolism in photosynthetic and nonphotosynthetic plant cells.

AraGEM is a viable framework for in silico functional analysis and can be used to derive new, nontrivial hypotheses for exploring plant metabolism. We take for granted that AraGEM is the genome-scale metabolic network model that currently better approximates the metabolism model of N. benthamiana. In Sexy Plant we have added in silico the reactions from the network of pheromone production. As optimality criterion we sought to maximize the pheromone flux produced by the plant.

Pheromone pathway location

Figure 1. Palmitic acid is a common fatty acid in plants and animals. This metabolite is the precursor of our pheromone.

Palmitic acid (16:0) is the most common fatty acid (saturated) found in animals, plants and microorganisms.

As precursor of our pathway, our efforts were aimed at the optimization of palmitic acid. In the AraGEM model, this is denoted as Hexadecanoic acid_acc (16:0) and is located in the cytosol (see Figure 1). To model the pathway, we introduced the reaction using one influx V1 and two effluxes V2, V3 (see Figure 2). The efflux V2 was incorporated as an exchange reaction, in order to generate a branch in the original pathway of 16:0 metabolism. As our metabolic pathway is linear, starting from 16:0, this new added branch represents the whole synthetic pathway of our pheromone.

Figure 2. In AraGEM, palmitic acid is also called Hexadecanoic32 Acid_acc. The reaction added ExZ11 produces the efflux V3 known as palmitic acidexchange.

Defining scenarios

AraGEM is capable of representing both photosynthetic and nonphotosynthetic cell types [1]. In order to reproduce the classical physiological scenarios of plant cell metabolism, we explored two photosynthetic scenarios: i) Photosynthesis and ii) Photorespiration. The difference comes from the carboxylation reaction of rubisco. This enzyme, in the presence of oxygen, reduces the energy efficiency of photosynthetic output by 25% in C3 plants.

Figure 3. The action of the rubisco enzyme defines two scenarios in plant metabolism: photosynthesis, and photorespiration. During photosynthesis, the carboxylation-oxygenation ratio is +1:0 and there is no oxygenation of ribulose 1.5-bisP. Moreover, the presence of oxygen and rubisco also catalyzes an oxygen reaction, photosynthesis efficiency is reduced, and the carboxylation-oxygenation ratio is +3:1.

Model assumptions

In plants, most genome-scale metabolic network reconstructions minimize the photons consumption (Ex16) while growth rate or biomass (BIO_L) rate is kept fixed. This is true if we mainly seek the survival of the plant. In such a case, photons consumption will be the optimization objective.

In our case, the principal objective is maximizing the pheromone production. In other words, optimizing the efflux V3 (see Figure 2) from the exchange reaction ExZ11. In addition, we must introduce the lower (lb) and upper (ub) bounds for each reaction. The bounds for the flux reactions Ex16, BIO_L and ExZ11 were fitted according to Table 1.

Table 1. Upper and lower bounds in AraGEM.

Optimal pheromone production using FBA

Table 2. FBA results in each scenario.

The optimum flux distribution is here defined as the flux distribution that maximizes palmitic acid flux, for a fixed rate of biomass synthesis, and free photon uptake.

The metabolic contrast between photosynthesis and photorespiration is illustrated in Figure 4. During photosynthesis (Figure 4A and 4B) we see an increase of the palmitic acid exchange flux when the photons uptake is unconstrained (actually allowing it to reach the default maximum flux in COBRA, i.e. 1000).

Even when the photons flux increases freely, most palmitic acid is used for plant growth. Therefore, the new palmitic acid_{exchange} flux only becomes 5.33 nM/seg. However, this low level is somehow forced by the high growth rate that was fixed according to the few existing literature references.

Figure 4. Optimization during photosynthesis with two different objectives fluxes A) minimizing photons uptake and B) maximizing palmitic acidexchange. During photorespiration, metabolism products decrease, such as C) photons uptake and D) palmitic acidexchange.

During photorespiration, we used FBA to optimize and analyze both palmitic acid exchange, and photons uptake. Figure 4C and 4D show an imperceptible loss (2%) in the palmitic acid exchange flux. The new flux is 5.24 nM/seg, similar to the one obtained in the photosynthesis scenario.

We also performed a supplementary analysis produced using gene knockout. COBRA toolbox was used to knock out genes of the AraGEM model on a one by one basis to optimize the palmitic acid exchange flux. The Figure 5 shows the maximum palmitic acid exchange flux obtained after gene knockout of each gene. Out of 1404 knocked out genes, both at photosynthesis and photorespiration, the optimal palmitic acid exchange flux decreases in 33 cases, and does not present improvement in the remaining ones.

Figure 5. Palmitic acid exchange flux after gene knockout. From 1404 genes in AraGEM model, 33 (pink lines) gene show an influence over the optimal palmitic acid exchange flux.

References