Fat synthesis in adipose tissue. An examination of stoichiometric constraints

Fell, David; Small, J. Rankin

doi:10.1042/bj2380781

Cited by 240 publications

(166 citation statements)

References 11 publications

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“…product formation per time unit) should be maximised [2,3,5] while others argued that molar yield (i.e. product formation per mole of substrate) should be maximised [64][65][66]. Both assumptions sound plausible.…”

Section: Discussionmentioning

confidence: 99%

Use of Game-Theoretical Methods in Biochemistry and Biophysics

et al. 2008

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Evolutionary game theory can be considered as an extension of the theory of evolutionary optimisation in that two or more organisms (or more generally, units of replication) tend to optimise their properties in an interdependent way. Thus, the outcome of the strategy adopted by one species (e.g., as a result of mutation and selection) depends on the strategy adopted by the other species. In this review, the use of evolutionary game theory for analysing biochemical and biophysical systems is discussed. The presentation is illustrated by a number of instructive examples such as the competition between microorganisms using different metabolic pathways for adenosine triphosphate production, the secretion of extracellular enzymes, the growth of trees and photosynthesis. These examples show that, due to conflicts of interest, the global optimum (in the sense of being the best solution for the whole system) is not always obtained. For example, some yeast species use metabolic pathways that waste nutrients, and in a dense tree canopy, trees grow taller than would be optimal for biomass productivity. From the viewpoint of game theory, the examples considered can be described by the Prisoner's Dilemma, snowdrift game, Tragedy of the Commons and rock-scissors-paper game.

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Section: Discussionmentioning

confidence: 99%

Use of Game-Theoretical Methods in Biochemistry and Biophysics

et al. 2008

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“…One early development was the use of linear programming to examine the constraints on metabolic function and product yields set by reaction stoichiometry and network structure (Fell and Small, 1986;Varma and Palsson, 1994), the methodology eventually becoming known by the term flux balance analysis (FBA) coined by the Palsson group (Varma and Palsson, 1994). This type of computational analysis is a more efficient and thorough replacement for older conventional approaches, which consisted of manual accounting of the stoichiometry of metabolic conversions along defined pathways.…”

Section: Modeling Metabolism Modeling Approachesmentioning

confidence: 99%

Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism

et al. 2013

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We describe the construction and analysis of a genome-scale metabolic model representing a developing leaf cell of rice (Oryza sativa) primarily derived from the annotations in the RiceCyc database. We used flux balance analysis to determine that the model represents a network capable of producing biomass precursors (amino acids, nucleotides, lipid, starch, cellulose, and lignin) in experimentally reported proportions, using carbon dioxide as the sole carbon source. We then repeated the analysis over a range of photon flux values to examine responses in the solutions. The resulting flux distributions show that (1) redox shuttles between the chloroplast, cytosol, and mitochondrion may play a significant role at low light levels, (2) photorespiration can act to dissipate excess energy at high light levels, and (3) the role of mitochondrial metabolism is likely to vary considerably according to the balance between energy demand and availability. It is notable that these organelle interactions, consistent with many experimental observations, arise solely as a result of the need for mass and energy balancing without any explicit assumptions concerning kinetic or other regulatory mechanisms.

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“…Building on these preexisting models, we developed a stoichiometric model reflecting metabolism in mint GTs by integrating newer transcriptome data sets with the wealth of knowledge on this subject in the published literature. We then employed a series of simulations, based on flux balance analysis (Fell and Small, 1986;Savinell and Palsson, 1992), to predict reactions with critical functions in monoterpene formation under extraordinarily high flux. Follow-up experimental testing revealed shared, carbon source-dependent roles for oxidative phosphorylation and ethanolic fermentation in ATP regeneration and the occurrence of a unique pair of ferredoxin (Fd) and ferredoxin-NADP + reductase (FNR) in heterotrophic peppermint GTs.…”

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confidence: 99%

Bioenergetics of Monoterpenoid Essential Oil Biosynthesis in Nonphotosynthetic Glandular Trichomes

et al. 2017

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ORCID IDs: 0000-0001-8261-9015 (S.R.J.); 0000-0001-7934-7987 (N.S.); 0000-0001-6565-9584 (B.M.L.).The commercially important essential oils of peppermint (Mentha 3 piperita) and its relatives in the mint family (Lamiaceae) are accumulated in specialized anatomical structures called glandular trichomes (GTs). A genome-scale stoichiometric model of secretory phase metabolism in peppermint GTs was constructed based on current biochemical and physiological knowledge. Fluxes through the network were predicted based on metabolomic and transcriptomic data. Using simulated reaction deletions, this model predicted that two processes, the regeneration of ATP and ferredoxin (in its reduced form), exert substantial control over flux toward monoterpenes. Follow-up biochemical assays with isolated GTs indicated that oxidative phosphorylation and ethanolic fermentation were active and that cooperation to provide ATP depended on the concentration of the carbon source. We also report that GTs with high flux toward monoterpenes express, at very high levels, genes coding for a unique pair of ferredoxin and ferredoxin-NADP + reductase isoforms. This study provides, to our knowledge, the first evidence of how bioenergetic processes determine flux through monoterpene biosynthesis in GTs.

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Fat synthesis in adipose tissue. An examination of stoichiometric constraints

Cited by 240 publications

References 11 publications

Use of Game-Theoretical Methods in Biochemistry and Biophysics

Use of Game-Theoretical Methods in Biochemistry and Biophysics

Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism

Bioenergetics of Monoterpenoid Essential Oil Biosynthesis in Nonphotosynthetic Glandular Trichomes

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