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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.


One of the possible pathways for chlorophyll biosynthesis in plants.Reactions marked in red are the essential reactions (including transporters). For reactions numbered 1–15 refer Supplementary Figure S1 online. The three compartments, i.e. chloroplast, mitochondria and the cytosol were found to be involved in chlorophyll synthesis pathway. When Rubisco oxygenase activity comes into play, the peroxisome is also involved in the process, wherein a few of the photorespiratory reactions are also found to be essential. Bold purple arrow heads indicate the reactions involved when Rubisco carboxylase and oxygenase was set at 3:1, broken purple arrows indicate peroxisomal transporters. Methyl cycle is found to be essentially linked with chlorophyll synthesis. Intermediates: 3-P-HydP, 3-P-HYDROXYPYRUVATE; 3-P-Ser, 3-PHOSPHO-SERINE; HP, Hydrogen-peroxide; OH-Pyr, Hydroxy-pyruvate; 2OG, oxoglutarate; SAM, S-AdenosylMethionine; AdoHcy, AdenosylHomoCysteine; Hcy, homocysteine; Gly, glycine; AlphaKG , Alpha-ketoglutarate/oxoglutarate; Ser, serine; PEP, phosphoenol pyruvate; OAA, oxaloacetate; Mal, malate; Glu, glutamate; Gln, glutamine; Pyr,pyruvate; THF,tetrahydrofolate; MeTHF,5,10-methylenetetrahydrofolate; 5-MeTHF,5-methyltetrahydrofolate; MET,methionine. Enzymes of methyl cycle: 1, 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase; 2, 5,10-methylenetetrahydrofolate reductase; 3, methionine synthase; 4, S-adenosylmethionine synthetase; 5, adenosylhomocysteinase. Enzymes: GS2, chloroplastic glutamine synthetase; GS1, cytosolic glutamine synthetase. External metabolites: x_CO2- external carbon-dioxide; x_Ammonia- external ammonia. _tx indicate the transporters. Reactions marked *are the reactions found to be essential but no supporting literature is available.
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f1: One of the possible pathways for chlorophyll biosynthesis in plants.Reactions marked in red are the essential reactions (including transporters). For reactions numbered 1–15 refer Supplementary Figure S1 online. The three compartments, i.e. chloroplast, mitochondria and the cytosol were found to be involved in chlorophyll synthesis pathway. When Rubisco oxygenase activity comes into play, the peroxisome is also involved in the process, wherein a few of the photorespiratory reactions are also found to be essential. Bold purple arrow heads indicate the reactions involved when Rubisco carboxylase and oxygenase was set at 3:1, broken purple arrows indicate peroxisomal transporters. Methyl cycle is found to be essentially linked with chlorophyll synthesis. Intermediates: 3-P-HydP, 3-P-HYDROXYPYRUVATE; 3-P-Ser, 3-PHOSPHO-SERINE; HP, Hydrogen-peroxide; OH-Pyr, Hydroxy-pyruvate; 2OG, oxoglutarate; SAM, S-AdenosylMethionine; AdoHcy, AdenosylHomoCysteine; Hcy, homocysteine; Gly, glycine; AlphaKG , Alpha-ketoglutarate/oxoglutarate; Ser, serine; PEP, phosphoenol pyruvate; OAA, oxaloacetate; Mal, malate; Glu, glutamate; Gln, glutamine; Pyr,pyruvate; THF,tetrahydrofolate; MeTHF,5,10-methylenetetrahydrofolate; 5-MeTHF,5-methyltetrahydrofolate; MET,methionine. Enzymes of methyl cycle: 1, 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase; 2, 5,10-methylenetetrahydrofolate reductase; 3, methionine synthase; 4, S-adenosylmethionine synthetase; 5, adenosylhomocysteinase. Enzymes: GS2, chloroplastic glutamine synthetase; GS1, cytosolic glutamine synthetase. External metabolites: x_CO2- external carbon-dioxide; x_Ammonia- external ammonia. _tx indicate the transporters. Reactions marked *are the reactions found to be essential but no supporting literature is available.

Mentions: Using FBA we identified one of the possible pathways for chlorophyll synthesis (Fig. 1).


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

Chatterjee A, Kundu S - Sci Rep (2015)

One of the possible pathways for chlorophyll biosynthesis in plants.Reactions marked in red are the essential reactions (including transporters). For reactions numbered 1–15 refer Supplementary Figure S1 online. The three compartments, i.e. chloroplast, mitochondria and the cytosol were found to be involved in chlorophyll synthesis pathway. When Rubisco oxygenase activity comes into play, the peroxisome is also involved in the process, wherein a few of the photorespiratory reactions are also found to be essential. Bold purple arrow heads indicate the reactions involved when Rubisco carboxylase and oxygenase was set at 3:1, broken purple arrows indicate peroxisomal transporters. Methyl cycle is found to be essentially linked with chlorophyll synthesis. Intermediates: 3-P-HydP, 3-P-HYDROXYPYRUVATE; 3-P-Ser, 3-PHOSPHO-SERINE; HP, Hydrogen-peroxide; OH-Pyr, Hydroxy-pyruvate; 2OG, oxoglutarate; SAM, S-AdenosylMethionine; AdoHcy, AdenosylHomoCysteine; Hcy, homocysteine; Gly, glycine; AlphaKG , Alpha-ketoglutarate/oxoglutarate; Ser, serine; PEP, phosphoenol pyruvate; OAA, oxaloacetate; Mal, malate; Glu, glutamate; Gln, glutamine; Pyr,pyruvate; THF,tetrahydrofolate; MeTHF,5,10-methylenetetrahydrofolate; 5-MeTHF,5-methyltetrahydrofolate; MET,methionine. Enzymes of methyl cycle: 1, 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase; 2, 5,10-methylenetetrahydrofolate reductase; 3, methionine synthase; 4, S-adenosylmethionine synthetase; 5, adenosylhomocysteinase. Enzymes: GS2, chloroplastic glutamine synthetase; GS1, cytosolic glutamine synthetase. External metabolites: x_CO2- external carbon-dioxide; x_Ammonia- external ammonia. _tx indicate the transporters. Reactions marked *are the reactions found to be essential but no supporting literature is available.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: One of the possible pathways for chlorophyll biosynthesis in plants.Reactions marked in red are the essential reactions (including transporters). For reactions numbered 1–15 refer Supplementary Figure S1 online. The three compartments, i.e. chloroplast, mitochondria and the cytosol were found to be involved in chlorophyll synthesis pathway. When Rubisco oxygenase activity comes into play, the peroxisome is also involved in the process, wherein a few of the photorespiratory reactions are also found to be essential. Bold purple arrow heads indicate the reactions involved when Rubisco carboxylase and oxygenase was set at 3:1, broken purple arrows indicate peroxisomal transporters. Methyl cycle is found to be essentially linked with chlorophyll synthesis. Intermediates: 3-P-HydP, 3-P-HYDROXYPYRUVATE; 3-P-Ser, 3-PHOSPHO-SERINE; HP, Hydrogen-peroxide; OH-Pyr, Hydroxy-pyruvate; 2OG, oxoglutarate; SAM, S-AdenosylMethionine; AdoHcy, AdenosylHomoCysteine; Hcy, homocysteine; Gly, glycine; AlphaKG , Alpha-ketoglutarate/oxoglutarate; Ser, serine; PEP, phosphoenol pyruvate; OAA, oxaloacetate; Mal, malate; Glu, glutamate; Gln, glutamine; Pyr,pyruvate; THF,tetrahydrofolate; MeTHF,5,10-methylenetetrahydrofolate; 5-MeTHF,5-methyltetrahydrofolate; MET,methionine. Enzymes of methyl cycle: 1, 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase; 2, 5,10-methylenetetrahydrofolate reductase; 3, methionine synthase; 4, S-adenosylmethionine synthetase; 5, adenosylhomocysteinase. Enzymes: GS2, chloroplastic glutamine synthetase; GS1, cytosolic glutamine synthetase. External metabolites: x_CO2- external carbon-dioxide; x_Ammonia- external ammonia. _tx indicate the transporters. Reactions marked *are the reactions found to be essential but no supporting literature is available.
Mentions: Using FBA we identified one of the possible pathways for chlorophyll synthesis (Fig. 1).

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.