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Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): Aiming to increase biomass

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Abstract

Due to socio-economic reasons, it is essential to design efficient stress-tolerant, more nutritious, high yielding rice varieties. A systematic understanding of the rice cellular metabolism is essential for this purpose. Here, we analyse a genome-scale metabolic model of rice leaf using Flux Balance Analysis to investigate whether it has potential metabolic flexibility to increase the biosynthesis of any of the biomass components. We initially simulate the metabolic responses under an objective to maximize the biomass components. Using the estimated maximum value of biomass synthesis as a constraint, we further simulate the metabolic responses optimizing the cellular economy. Depending on the physiological conditions of a cell, the transport capacities of intracellular transporters (ICTs) can vary. To mimic this physiological state, we randomly vary the ICTs’ transport capacities and investigate their effects. The results show that the rice leaf has the potential to increase glycine and starch in a wide range depending on the ICTs’ transport capacities. The predicted biosynthesis pathways vary slightly at the two different optimization conditions. With the constraint of biomass composition, the cell also has the metabolic plasticity to fix a wide range of carbon-nitrogen ratio.

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Abbreviations

AcCoA:

Acetyl-CoA

AlphaKG/α-KG/2-KG:

alpha/2 ketoglutarate

BPGA:

1,3 bisphospho-D-glycerate

Cit:

citrate

CisAconitate:

cis-aconitate

CoA:

Coenzyme A

Cyt_ox:

cytochrome c oxidase

Cyt_red:

cytochrome c reductase

DHAP:

dihydroxy-acetone phosphate

ETC:

electron transport chain

E4P:

erythrose-4 phosphate

FBP:

fructose 1,6 bisphosphate

Fum:

Fumarate

F6P:

fructose 6-phosphate

GAP:

glyceraldehyde 3-phosphate

GLT:

glutamate

Gly:

glycine

G1P:

glucose 1-phosphate

G6P:

glucose 6-phosphate

Homo-Ser:

homoserine

IsoCitrate:

isocitrate

Mal:

Malate

MalOxAc:

malate oxaloacetate

OAA:

oxaloacetate

PEP:

phosphoenolpyruvate

PGA:

3-phosphoglycerate

PGA2:

2-phosphoglycerate

PGly:

Phosphoglycolate

Pi:

inorganic phosphate

PPi:

pyrophosphate

Pyr:

Pyruvate

Q:

ubiquinone

QH2:

ubiquinol

RuBP:

ribulose-1,5,-bisphosphate

Ru5P:

ribulose-5-phosphate

R5P:

ribose-5-phosphate

SBP:

sedoheptulose-1,7-bisphosphatase

suc:

succinate

SucCoA:

succinyl-CoA

S7P:

sedoheptulose-7-phosphate

THR:

threonine

X5P:

xylulose-5-phosphate

_ext:

external

_int:

internal

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Acknowledgements

RS would like to thank Council of Scientific and Industrial Research (CSIR), India, for the fellowship (Sanction No. 028(0922)/2014-EMR-I). The authors would like to thank Center of Excellence (CoE) in Systems Biology and Biomedical engineering (A TEQIP-II Project), University of Calcutta for financial assistance.

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Authors and Affiliations

  1. Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 APC Road, Kolkata, 700009, India

    Rahul Shaw & Sudip Kundu

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  1. Rahul Shaw
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  2. Sudip Kundu
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Correspondence to Sudip Kundu.

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[Shaw R and Kundu S 2015 Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): Aiming to increase biomass. J. Biosci.] DOI 10.1007/s12038-015-9563-z

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Shaw, R., Kundu, S. Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): Aiming to increase biomass. J Biosci 40, 819–828 (2015). https://doi.org/10.1007/s12038-015-9563-z

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  • DOI: https://doi.org/10.1007/s12038-015-9563-z

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