研究领域

Metabolic network analysis

Metabolic networks supply the precursors, energy and reducing power required for the synthesis and turnover of cellular components. The associated flows of material – the metabolic fluxes – are crucial in determining the performance and productivity of cells and organisms. For example, in an agricultural context, the production of harvestable end-products of plant metabolism is entirely dependent on the flux phenotype of the plant; while in biotechnology, the exploitation of micro-organisms and plants hinges on an ability to reconfigure the metabolic network to favour a flux distribution that leads to the preferential synthesis of particular products. Thus the fluxes supported by the plant metabolic network play a pivotal role in determining both phenotype and productivity. My main interest lies in understanding the organisation and regulation of the metabolic fluxes that occur in the plant metabolic network. A knowledge of the transcriptome, proteome or metabolome does not lead easily to the metabolic flux phenotype, and internal fluxes within the metabolic network have to be deduced from a suite of computational and experimental tools. My research group is strongly involved in the development and application of steady-state metabolic flux analysis (MFA), a technique that allows fluxes to be deduced from a stoichiometric model of the network using stable isotope (13C) labelling data and measurements of biosynthetic outputs. We complement this MFA work with an in silico approach using genome-scale models and constraints-based flux balance analysis. Together these methods allow us to assess the metabolic phenotypes of wild type, mutant and transgenic plants, and thus the metabolic impact of genetic and environmental perturbations.

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S.L. McCraw, D.H. Park, R. Jones, M. Bentley, A. Rico, R.G. Ratcliffe, N.J. Kruger, A. Collmer and G.M. Preston (2017) GABA uptake via the GABA permease GabP represses virulence gene expression in Pseudomonas syringae pv. tomato DC3000. Molecular Plant-Microbe Interactions in press. K.J. Gupta, C.P. Lee and R.G. Ratcliffe (2016) Nitrite protects mitochondrial structure and function under hypoxia. Plant and Cell Physiology in press. J.J. Terpolilli, S.K. Masakapalli, R. Karunakaran, I. Webb, R. Green, N.J. Watmough, N.J. Kruger, R.G. Ratcliffe and P.S. Poole (2016) Lipogenesis and redox balance in nitrogen-fixing pea bacteroids. Journal of Bacteriology 198, 2864-2875. C.Y.M. Cheung, R.G. Ratcliffe and L.J. Sweetlove (2015) A method of accounting for enzyme costs in flux balance analysis reveals alternative pathways and metabolite stores in an illuminated Arabidopsis leaf. Plant Physiology 169, 1671-1682. B. Royo, J.F. Morán, R.G. Ratcliffe and K.J. Gupta (2015) Nitric oxide induces the alternative oxidase pathway in Arabidopsis seedlings deprived of inorganic phosphate. Journal of Experimental Botany 66, 6273-6280. N.J. Kruger and R.G. Ratcliffe (2015) Fluxes through plant metabolic networks: measurements, predictions, insights and challenges. Biochemical Journal 465, 27-38. A.U. Igamberdiev, R.G. Ratcliffe and K.J. Gupta (2014) Plant mitochondria: source and target for nitric oxide. Mitochondrion 19, 329-333. K.J. Gupta, L.A.J. Mur and R.G. Ratcliffe (2014) Guarding the guard cells? New Phytologist 203, 349-351. S.K. Masakapalli, N.J. Kruger and R.G. Ratcliffe (2014) The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation. The Plant Journal 78, 964-977. C.Y.M. Cheung, M.G. Poolman, D.A. Fell, R.G. Ratcliffe and L.J. Sweetlove (2014) A diel flux-balance model captures interactions between light and dark metabolism during day-night cycles in C3 and CAM leaves. Plant Physiology 165, 917-929. B.L. Møller and R.G. Ratcliffe (2014) Synthetic plant biology: the roots of a bio-based society. Current Opinion in Biotechnology 26, ix-xvi. K.J. Gupta, K.H. Hebelstrup, N.J. Kruger and R.G. Ratcliffe (2014) Nitric oxide is required for homeostasis of oxygen and reactive oxygen species in barley roots under aerobic conditions. Molecular Plant 7, 747-750. S.K. Masakapalli, A. Ritala, L. Dong, A.R. van der Krol, K.M. Oksman-Caldentey, R.G. Ratcliffe and L.J. Sweetlove (2014) Metabolic flux phenotype of tobacco hairy roots engineered for increased geraniol production. Phytochemistry 99, 73-85. S.K. Masakapalli, R.G. Ratcliffe and T.C.R. Williams (2014) Quantification of 13C enrichments and isotopomer abundances for metabolic flux analysis using 1D NMR spectroscopy. In Plant Metabolic Flux Analysis: Methods and Protocols (eds M. Dieuaide-Noubhani and A.P. Alonso), Methods in Molecular Biology 1090, 73-86.