title: Metabolic Plasticity and Inter-Compartmental Interactions in Rice Metabolism: An Analysis from Reaction Deletion Study.
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.
authors.affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 APC Road, Kolkata 700009, West Bengal, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Shaw
authors.affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 APC Road, Kolkata 700009, West Bengal, India; Centre of Excellence in Systems Biology & Biomedical Engineering, (TEQIP, Phase-II), University of Calcutta, 92 APC Road, Kolkata 700009, West Bengal, India.
authors.forename: Sudip
authors.initials: S
authors.lastname: Kundu
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D018533:Biomass; D002736:Chloroplasts / Q000378:metabolism / Q000528:radiation effects; D003600:Cytosol / Q000378:metabolism / Q000528:radiation effects; D005838:Genotype; D064688:Metabolic Flux Analysis; D053858:Metabolic Networks and Pathways; D008928:Mitochondria / Q000378:metabolism / Q000528:radiation effects; D009249:NADP / Q000378:metabolism; D012275:Oryza / Q000166:cytology / Q000235:genetics / Q000378:metabolism* / Q000528:radiation effects; D017785:Photons; D010788:Photosynthesis / Q000528:radiation effects
chemical_list: D009249:NADP; D000255:Adenosine Triphosphate