title: Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): aiming to increase biomass.
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.
authors.affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 APC Road, Kolkata 700009, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Shaw
authors.forename: Sudip
authors.initials: S
authors.lastname: Kundu
mesh_terms: D000465:Algorithms; D018533:Biomass; D002244:Carbon / Q000378:metabolism; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D002736:Chloroplasts / Q000235:genetics / Q000378:metabolism; D018556:Crops, Agricultural / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D018745:Genome, Plant; D005998:Glycine / Q000096:biosynthesis; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008954:Models, Biological; D009584:Nitrogen / Q000378:metabolism; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D013213:Starch / Q000096:biosynthesis
chemical_list: D002352:Carrier Proteins; D010940:Plant Proteins; D002244:Carbon; D013213:Starch; D009584:Nitrogen; D005998:Glycine