Metabolic trade-offs between biomass synthesis and photosynthate export at different light intensities in a genome-scale metabolic model of rice.

Mark G Poolman,Rahul Shaw,David A Fell,Sudip Kundu

doi:10.3389/fpls.2014.00656

Mark G Poolman, Rahul Shaw + Show 2 more

Open Access

https://doi.org/10.3389/fpls.2014.00656

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Abstract

Previously we have used a genome scale model of rice metabolism to describe how metabolism reconfigures at different light intensities in an expanding leaf of rice. Although this established that the metabolism of the leaf was adequately represented, in the model, the scenario was not that of the typical function of the leaf—to provide material for the rest of the plant. Here we extend our analysis to explore the transition to a source leaf as export of photosynthate increases at the expense of making leaf biomass precursors, again as a function of light intensity. In particular we investigate whether, when the leaf is making a smaller range of compounds for export to the phloem, the same changes occur in the interactions between mitochondrial and chloroplast metabolism as seen in biomass synthesis for growth when light intensity increases. Our results show that the same changes occur qualitatively, though there are slight quantitative differences reflecting differences in the energy and redox requirements for the different metabolic outputs.

Highlights

Genome–scale metabolic modeling (GSM) is a technique for investigating the feasible metabolic states of an organism, taking account of the possibilities and constraints imposed by the structure of the metabolic network
The principal constraint is that of mass balance, dictated by the stoichiometries of the reactions in the network, coupled with the assumption of a metabolic steady state where the production and consumption of all internal metabolites of the network is balanced so that their concentrations remain constant. This defines a space containing all feasible states of the metabolism, from which more specific solutions are extracted with a combination of additional constraints, such as experimentally-observed values of nutrient uptake and growth rates, with an objective function that is intended to define an optimal state of the metabolism
Our results have shown that the occurrence of transitions in the flux solutions for our rice leaf cell metabolism model at different light intensities are not peculiar to the production of a specific metabolic output, but are relatively insensitive to the nature of the output

Summary

Introduction

Genome–scale metabolic modeling (GSM) is a technique for investigating the feasible metabolic states of an organism, taking account of the possibilities and constraints imposed by the structure of the metabolic network. The principal constraint is that of mass balance, dictated by the stoichiometries of the reactions in the network, coupled with the assumption of a metabolic steady state where the production and consumption of all internal metabolites of the network is balanced so that their concentrations remain constant. This defines a space containing all feasible states of the metabolism, from which more specific solutions are extracted with a combination of additional constraints, such as experimentally-observed values of nutrient uptake and growth rates, with an objective function that is intended to define an optimal state of the metabolism. The models are solved using linear programming, and associated techniques that are part of the methodology known as Flux Balance Analysis (FBA), to give a predicted distribution of fluxes in the metabolic network

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