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Metabolic Plasticity and Inter-Compartmental Interactions in Rice Metabolism: An Analysis from Reaction Deletion Study.

Shaw R, Kundu S - PLoS ONE (2015)

Bottom Line: While some of the alternative paths are energetically equally efficient, others demand for higher photon.The variations in (i) ATP/NADPH ratio, (ii) exchange of metabolites through chloroplastic transporters and (iii) total biomass production are also presented here.Mutual metabolic dependencies of different cellular compartments are also demonstrated.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 APC Road, Kolkata 700009, West Bengal, India.

ABSTRACT
More than 20% of the total caloric intake of human population comes from rice. The expression of rice genes and hence, the concentration of enzymatic proteins might vary due to several biotic and abiotic stresses. It in turn, can influence the overall metabolism and survivability of rice plant. Thus, understanding the rice cellular metabolism, its plasticity and potential readjustments under different perturbations can help rice biotechnologists to design efficient rice cultivars. Here, using the flux balance analysis (FBA) method, with the help of in-silico reaction deletion strategy, we study the metabolic plasticity of genome-scale metabolic model of rice leaf. A set of 131 reactions, essential for the production of primary biomass precursors is identified; deletion of any of them can inhibit the overall biomass production. Usability Index (IU) for the rest of the reactions are estimated and based on this parameter, they are classified into three categories-maximally-favourable, quasi-favourable and unfavourable for the primary biomass production. The lower value of 1 - IU of a reaction suggests that the cell cannot easily bypass it for biomass production. While some of the alternative paths are energetically equally efficient, others demand for higher photon. The variations in (i) ATP/NADPH ratio, (ii) exchange of metabolites through chloroplastic transporters and (iii) total biomass production are also presented here. Mutual metabolic dependencies of different cellular compartments are also demonstrated.

No MeSH data available.


Variation of ATP/NADPH ratio due to deletions of reactions.ATP and NADPH produced in the light reactions are calculated by the their stoichiometric coefficient times the flux of the light reactions. Deletions of a few mitochondrial and chloroplastic reactions (shown by down arrow) increase the ATP/NADPH ratio.
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pone.0133899.g006: Variation of ATP/NADPH ratio due to deletions of reactions.ATP and NADPH produced in the light reactions are calculated by the their stoichiometric coefficient times the flux of the light reactions. Deletions of a few mitochondrial and chloroplastic reactions (shown by down arrow) increase the ATP/NADPH ratio.

Mentions: Several MT metabolic states need higher amount of energy as well as reductant to maintain the cellular processes required for biomass production in the absence of favourable reactions (Figs 2 and 6). This section demonstrates how the cell readjusts its metabolism using alternative biochemical pathways (and consequently generates and utilizes different amounts of ATP and NADPH) optimizing the cellular economy.


Metabolic Plasticity and Inter-Compartmental Interactions in Rice Metabolism: An Analysis from Reaction Deletion Study.

Shaw R, Kundu S - PLoS ONE (2015)

Variation of ATP/NADPH ratio due to deletions of reactions.ATP and NADPH produced in the light reactions are calculated by the their stoichiometric coefficient times the flux of the light reactions. Deletions of a few mitochondrial and chloroplastic reactions (shown by down arrow) increase the ATP/NADPH ratio.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4519304&req=5

pone.0133899.g006: Variation of ATP/NADPH ratio due to deletions of reactions.ATP and NADPH produced in the light reactions are calculated by the their stoichiometric coefficient times the flux of the light reactions. Deletions of a few mitochondrial and chloroplastic reactions (shown by down arrow) increase the ATP/NADPH ratio.
Mentions: Several MT metabolic states need higher amount of energy as well as reductant to maintain the cellular processes required for biomass production in the absence of favourable reactions (Figs 2 and 6). This section demonstrates how the cell readjusts its metabolism using alternative biochemical pathways (and consequently generates and utilizes different amounts of ATP and NADPH) optimizing the cellular economy.

Bottom Line: While some of the alternative paths are energetically equally efficient, others demand for higher photon.The variations in (i) ATP/NADPH ratio, (ii) exchange of metabolites through chloroplastic transporters and (iii) total biomass production are also presented here.Mutual metabolic dependencies of different cellular compartments are also demonstrated.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 APC Road, Kolkata 700009, West Bengal, India.

ABSTRACT
More than 20% of the total caloric intake of human population comes from rice. The expression of rice genes and hence, the concentration of enzymatic proteins might vary due to several biotic and abiotic stresses. It in turn, can influence the overall metabolism and survivability of rice plant. Thus, understanding the rice cellular metabolism, its plasticity and potential readjustments under different perturbations can help rice biotechnologists to design efficient rice cultivars. Here, using the flux balance analysis (FBA) method, with the help of in-silico reaction deletion strategy, we study the metabolic plasticity of genome-scale metabolic model of rice leaf. A set of 131 reactions, essential for the production of primary biomass precursors is identified; deletion of any of them can inhibit the overall biomass production. Usability Index (IU) for the rest of the reactions are estimated and based on this parameter, they are classified into three categories-maximally-favourable, quasi-favourable and unfavourable for the primary biomass production. The lower value of 1 - IU of a reaction suggests that the cell cannot easily bypass it for biomass production. While some of the alternative paths are energetically equally efficient, others demand for higher photon. The variations in (i) ATP/NADPH ratio, (ii) exchange of metabolites through chloroplastic transporters and (iii) total biomass production are also presented here. Mutual metabolic dependencies of different cellular compartments are also demonstrated.

No MeSH data available.