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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.


The deletion effect of PHOSPHOGLUCMUT-RXN is shown here.The WT shows the pathway by PHOSPHOGLUCMUT-RXN to synthesize cellulose. While deleted PHOSPHOGLUCMUT-RXN, the alternative possible route via myo-inositol pathway to produce cellulose is shown in MT.
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pone.0133899.g005: The deletion effect of PHOSPHOGLUCMUT-RXN is shown here.The WT shows the pathway by PHOSPHOGLUCMUT-RXN to synthesize cellulose. While deleted PHOSPHOGLUCMUT-RXN, the alternative possible route via myo-inositol pathway to produce cellulose is shown in MT.

Mentions: We have observed that there are 13 maximally-favourable reactions (1 − IU ∼ 0) which show photon FC > 1 when deleted (S2 Dataset). Nine of them are presented in Table 2 for further discussions. Absence of any of them diverts the cellular metabolism into higher energy demanding pathways. Higher FC in photon usage can occur by two ways: (i) either the removed reaction is used to generate energy [ATP or NADP(H)] or (ii) its deletion causes diversion into energy demanding paths (thus, higher photon demanding paths) as shown in the Figs 4 and 5, respectively.


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

Shaw R, Kundu S - PLoS ONE (2015)

The deletion effect of PHOSPHOGLUCMUT-RXN is shown here.The WT shows the pathway by PHOSPHOGLUCMUT-RXN to synthesize cellulose. While deleted PHOSPHOGLUCMUT-RXN, the alternative possible route via myo-inositol pathway to produce cellulose is shown in MT.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133899.g005: The deletion effect of PHOSPHOGLUCMUT-RXN is shown here.The WT shows the pathway by PHOSPHOGLUCMUT-RXN to synthesize cellulose. While deleted PHOSPHOGLUCMUT-RXN, the alternative possible route via myo-inositol pathway to produce cellulose is shown in MT.
Mentions: We have observed that there are 13 maximally-favourable reactions (1 − IU ∼ 0) which show photon FC > 1 when deleted (S2 Dataset). Nine of them are presented in Table 2 for further discussions. Absence of any of them diverts the cellular metabolism into higher energy demanding pathways. Higher FC in photon usage can occur by two ways: (i) either the removed reaction is used to generate energy [ATP or NADP(H)] or (ii) its deletion causes diversion into energy demanding paths (thus, higher photon demanding paths) as shown in the Figs 4 and 5, respectively.

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.