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Multi-level kinetic model explaining diverse roles of isozymes in prokaryotes.

ABSTRACT: Current standard methods for kinetic and genomic modeling cannot provide deep insight into metabolic regulation. Here, we developed and evaluated a multi-scale kinetic modeling approach applicable to any prokaryote. Specifically, we highlight the primary metabolism of the cyanobacterium Synechococcus elongatus PCC 7942. The model bridges metabolic data sets from cells grown at different CO2 conditions by integrating transcriptomic data and isozymes. Identification of the regulatory roles of isozymes allowed the calculation and explanation of the absolute metabolic concentration of 3-phosphoglycerate. To demonstrate that this method can characterize any isozyme, we determined the function of two glycolytic glyceraldehyde-3-phosphate dehydrogenases: one co-regulates high concentrations of the 3-phosphoglycerate, the other shifts the bifurcation point in hexose regulation, and both improve biomass production. Moreover, the regulatory roles of multiple phosphoglycolate phosphatases were defined for varying (non-steady) CO2 conditions, suggesting their protective role against toxic photorespiratory intermediates.

SUBMITTER: Jablonsky J

PROVIDER: S-EPMC4138046 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Multi-level kinetic model explaining diverse roles of isozymes in prokaryotes.

Jablonsky Jiri J Schwarz Doreen D Hagemann Martin M

PloS one 20140815 8

Current standard methods for kinetic and genomic modeling cannot provide deep insight into metabolic regulation. Here, we developed and evaluated a multi-scale kinetic modeling approach applicable to any prokaryote. Specifically, we highlight the primary metabolism of the cyanobacterium Synechococcus elongatus PCC 7942. The model bridges metabolic data sets from cells grown at different CO2 conditions by integrating transcriptomic data and isozymes. Identification of the regulatory roles of isoz ...[more]

PMID: 25127487

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Project description:This article describes the data, data flows, and spreadsheet implementations for linking multi-level contribution margin accounting as a subsystem in cost accounting with several versions of a multi-level fixed-charge problem (MLFCP), the latter based on the optimization approach in operations research. This linkage can reveal previously hidden optimization potentials within the framework of multi-level contribution margin accounting, thus providing better information for decision making in companies and other organizations. For the data, plausible fictitious values have been assumed taking into consideration the calculation principles in cost accounting where applicable. They include resource-related data, market-related data, and data from cost accounting needed to analyze the profitability of a company´s products and organizational entities in the presence of hierarchically structured fixed costs. The data are processed and analyzed by means of mathematical optimization techniques and sensitivity analysis. The linkage between multi-level contribution margin accounting and MLFCP is implemented in three spreadsheet files, including versions for deterministic optimization, stochastic optimization, and robust optimization. This paper provides specifications for compatible solver add-ins and for executing sensitivity analysis. The data and spreadsheet implementations described in this article were used in a research article entitled "Making better decisions by applying mathematical optimization to cost accounting: An advanced approach to multi-level contribution margin accounting" [1]. The data sets and the spreadsheet implementations may be reused a) by researchers in management and cost accounting as well as in operations research and quantitative methods for verification and for further development of the linkage concept and of the underlying optimization models; b) by practitioners for gaining insight into the data requirements, methods, and benefits of the proposed linkage, thus supporting continuing education; and c) by instructors in academia who may find the data and spreadsheets valuable for classroom use in advanced courses. The complete spreadsheet implementations in the form of three ready-to-use Excel files (deterministic, stochastic, and robust version) are available for download at Mendeley Data. They may serve as customizable templates for various use cases in research, practice, and education.

Dataset Information

Multi-level kinetic model explaining diverse roles of isozymes in prokaryotes.

Publications

Multi-level kinetic model explaining diverse roles of isozymes in prokaryotes.

Similar Datasets

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