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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.


Up/down regulation of reactions/paths of one compartment when a reaction from another compartment is deleted.Reactions marked with UP/DN are deleted; and the color of UP/DN shows the flux increase (UP) or decrease (DN) in another compartment. For instance, when mit_MalDH is deleted, the chloroplastic malate oxaloacetate shuttle (represented by blue UP) up regulates and the F6P to G6P conversion (represented by green DN) in chloroplast down-regulates. Malate oxaloacetate shuttle in mitochondria becomes reverse of the shown direction when complexes I, V or mitochondrial O2 is removed. Although deletion of the reactions shown here causes high up/down regulation in flux in the same compartment or in cytosol but here we focused to observe maximum flux FC in different compartment i.e., change in mitochondria when chloroplastic reaction is deleted and vice versa. Here, CoA, Pyr, IsoCit, α-KG, AcCoA, Cit, Cyt_red, Cyt_ox, Q, QH2, MalOxAc, _ext and _int indicate Coenzyme A, Pyruvate, isocitrate, alpha ketoglutarate, Acetyl-CoA, citrate, cytochrome c reductase, cytochrome c oxidase, ubiquinone, ubiquinol, malate oxaloacetate, external and internal, respectively.
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pone.0133899.g008: Up/down regulation of reactions/paths of one compartment when a reaction from another compartment is deleted.Reactions marked with UP/DN are deleted; and the color of UP/DN shows the flux increase (UP) or decrease (DN) in another compartment. For instance, when mit_MalDH is deleted, the chloroplastic malate oxaloacetate shuttle (represented by blue UP) up regulates and the F6P to G6P conversion (represented by green DN) in chloroplast down-regulates. Malate oxaloacetate shuttle in mitochondria becomes reverse of the shown direction when complexes I, V or mitochondrial O2 is removed. Although deletion of the reactions shown here causes high up/down regulation in flux in the same compartment or in cytosol but here we focused to observe maximum flux FC in different compartment i.e., change in mitochondria when chloroplastic reaction is deleted and vice versa. Here, CoA, Pyr, IsoCit, α-KG, AcCoA, Cit, Cyt_red, Cyt_ox, Q, QH2, MalOxAc, _ext and _int indicate Coenzyme A, Pyruvate, isocitrate, alpha ketoglutarate, Acetyl-CoA, citrate, cytochrome c reductase, cytochrome c oxidase, ubiquinone, ubiquinol, malate oxaloacetate, external and internal, respectively.

Mentions: It is already known that the chloroplastic and mitochondrial metabolisms are highly dependent on each other and they serve some important cellular functions including ATP production and regulation of redox state in the cell [28–30]. Here, we have observed that the deletions of any of the mitochondrial electron transport chain reactions (mitochondrial complexes I, III, IV and V) show larger flux changes in the reaction associated with photon and consequently, these are associated with changes in the light non-cyclic and some times cyclic reactions (Table 2). Further, deletion of some other mitochondrial and cytosolic reactions also influence the fluxes of some of the chloroplastic reactions. The observations are presented in Fig 8 and summarized below.


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

Shaw R, Kundu S - PLoS ONE (2015)

Up/down regulation of reactions/paths of one compartment when a reaction from another compartment is deleted.Reactions marked with UP/DN are deleted; and the color of UP/DN shows the flux increase (UP) or decrease (DN) in another compartment. For instance, when mit_MalDH is deleted, the chloroplastic malate oxaloacetate shuttle (represented by blue UP) up regulates and the F6P to G6P conversion (represented by green DN) in chloroplast down-regulates. Malate oxaloacetate shuttle in mitochondria becomes reverse of the shown direction when complexes I, V or mitochondrial O2 is removed. Although deletion of the reactions shown here causes high up/down regulation in flux in the same compartment or in cytosol but here we focused to observe maximum flux FC in different compartment i.e., change in mitochondria when chloroplastic reaction is deleted and vice versa. Here, CoA, Pyr, IsoCit, α-KG, AcCoA, Cit, Cyt_red, Cyt_ox, Q, QH2, MalOxAc, _ext and _int indicate Coenzyme A, Pyruvate, isocitrate, alpha ketoglutarate, Acetyl-CoA, citrate, cytochrome c reductase, cytochrome c oxidase, ubiquinone, ubiquinol, malate oxaloacetate, external and internal, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133899.g008: Up/down regulation of reactions/paths of one compartment when a reaction from another compartment is deleted.Reactions marked with UP/DN are deleted; and the color of UP/DN shows the flux increase (UP) or decrease (DN) in another compartment. For instance, when mit_MalDH is deleted, the chloroplastic malate oxaloacetate shuttle (represented by blue UP) up regulates and the F6P to G6P conversion (represented by green DN) in chloroplast down-regulates. Malate oxaloacetate shuttle in mitochondria becomes reverse of the shown direction when complexes I, V or mitochondrial O2 is removed. Although deletion of the reactions shown here causes high up/down regulation in flux in the same compartment or in cytosol but here we focused to observe maximum flux FC in different compartment i.e., change in mitochondria when chloroplastic reaction is deleted and vice versa. Here, CoA, Pyr, IsoCit, α-KG, AcCoA, Cit, Cyt_red, Cyt_ox, Q, QH2, MalOxAc, _ext and _int indicate Coenzyme A, Pyruvate, isocitrate, alpha ketoglutarate, Acetyl-CoA, citrate, cytochrome c reductase, cytochrome c oxidase, ubiquinone, ubiquinol, malate oxaloacetate, external and internal, respectively.
Mentions: It is already known that the chloroplastic and mitochondrial metabolisms are highly dependent on each other and they serve some important cellular functions including ATP production and regulation of redox state in the cell [28–30]. Here, we have observed that the deletions of any of the mitochondrial electron transport chain reactions (mitochondrial complexes I, III, IV and V) show larger flux changes in the reaction associated with photon and consequently, these are associated with changes in the light non-cyclic and some times cyclic reactions (Table 2). Further, deletion of some other mitochondrial and cytosolic reactions also influence the fluxes of some of the chloroplastic reactions. The observations are presented in Fig 8 and summarized below.

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.