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Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica.

Chatterjee A, Kundu S - Sci Rep (2015)

Bottom Line: We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences.The focus of the present work is centered on rice leaf metabolism.Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air.

View Article: PubMed Central - PubMed

Affiliation: 1Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta India.

ABSTRACT
Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air.

No MeSH data available.


Activity of various intracellular transporters under combined activity of Rubisco carboxylase and oxygenase.Flux values marked in blue are the ones that were found to be same throughout the simulation under combined activity of Rubisco carboxylase and oxygenase. Similar to what we found under Rubisco carboxylase activity, same interlink was observed between chloroplastic GS and Mal-2OG transporter; chloroplastic ammonia transporter (x_am_tx) and chloroplastic Glu-Gln (the flux values increased due to photorespiration). In addition, the reactions of the peroxisome also were involved. (a) Fluxes through various transporters when flux through the chloroplastic ammonia transporter (ex_ammonia_tx) was set at 0 and 1 flux unit. (b) Fluxes through various transporters when flux through the chloroplastic ammonia transporter (ex_ammonia_tx) was set at 4 flux unit.
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f3: Activity of various intracellular transporters under combined activity of Rubisco carboxylase and oxygenase.Flux values marked in blue are the ones that were found to be same throughout the simulation under combined activity of Rubisco carboxylase and oxygenase. Similar to what we found under Rubisco carboxylase activity, same interlink was observed between chloroplastic GS and Mal-2OG transporter; chloroplastic ammonia transporter (x_am_tx) and chloroplastic Glu-Gln (the flux values increased due to photorespiration). In addition, the reactions of the peroxisome also were involved. (a) Fluxes through various transporters when flux through the chloroplastic ammonia transporter (ex_ammonia_tx) was set at 0 and 1 flux unit. (b) Fluxes through various transporters when flux through the chloroplastic ammonia transporter (ex_ammonia_tx) was set at 4 flux unit.

Mentions: For case 2, i.e. in the presence of Rubisco oxygenase activity, as expected to complete the C2 cycle, the fluxes through the chloroplastic transporter for Mal-Glu and Mal-2OG and the mitochondrial ammonia transporter, SHMT and GDC were much higher compared to what we obtained in case 1 (Fig. 3a).


Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica.

Chatterjee A, Kundu S - Sci Rep (2015)

Activity of various intracellular transporters under combined activity of Rubisco carboxylase and oxygenase.Flux values marked in blue are the ones that were found to be same throughout the simulation under combined activity of Rubisco carboxylase and oxygenase. Similar to what we found under Rubisco carboxylase activity, same interlink was observed between chloroplastic GS and Mal-2OG transporter; chloroplastic ammonia transporter (x_am_tx) and chloroplastic Glu-Gln (the flux values increased due to photorespiration). In addition, the reactions of the peroxisome also were involved. (a) Fluxes through various transporters when flux through the chloroplastic ammonia transporter (ex_ammonia_tx) was set at 0 and 1 flux unit. (b) Fluxes through various transporters when flux through the chloroplastic ammonia transporter (ex_ammonia_tx) was set at 4 flux unit.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595741&req=5

f3: Activity of various intracellular transporters under combined activity of Rubisco carboxylase and oxygenase.Flux values marked in blue are the ones that were found to be same throughout the simulation under combined activity of Rubisco carboxylase and oxygenase. Similar to what we found under Rubisco carboxylase activity, same interlink was observed between chloroplastic GS and Mal-2OG transporter; chloroplastic ammonia transporter (x_am_tx) and chloroplastic Glu-Gln (the flux values increased due to photorespiration). In addition, the reactions of the peroxisome also were involved. (a) Fluxes through various transporters when flux through the chloroplastic ammonia transporter (ex_ammonia_tx) was set at 0 and 1 flux unit. (b) Fluxes through various transporters when flux through the chloroplastic ammonia transporter (ex_ammonia_tx) was set at 4 flux unit.
Mentions: For case 2, i.e. in the presence of Rubisco oxygenase activity, as expected to complete the C2 cycle, the fluxes through the chloroplastic transporter for Mal-Glu and Mal-2OG and the mitochondrial ammonia transporter, SHMT and GDC were much higher compared to what we obtained in case 1 (Fig. 3a).

Bottom Line: We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences.The focus of the present work is centered on rice leaf metabolism.Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air.

View Article: PubMed Central - PubMed

Affiliation: 1Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta India.

ABSTRACT
Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air.

No MeSH data available.