Modeling the Calvin-Benson cycle

Jablonský, Jiří; Bauwe, Hermann

doi:10.1186/1752-0509-5-185

Cited by 37 publications

(23 citation statements)

References 31 publications

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“…The kinetic model, a successor of the corrected Zhu model [10], [11] of the Calvin-Benson cycle, was redesigned for cyanobacteria, extended (photorespiratory pathways, glycolysis) and validated on available metabolic data from Synechococcus el. PCC 7942 [6].…”

Section: Methodsmentioning

confidence: 99%

Phosphoglycerate Mutases Function as Reverse Regulated Isoenzymes in Synechococcus elongatus PCC 7942

Jablonský

Hagemann²,

Schwarz³

2013

PLoS ONE

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Phosphoglycerate-mutase (PGM) is an ubiquitous glycolytic enzyme, which in eukaryotic cells can be found in different compartments. In prokaryotic cells, several PGMs are annotated/localized in one compartment. The identification and functional characterization of PGMs in prokaryotes is therefore important for better understanding of metabolic regulation. Here we introduce a method, based on a multi-level kinetic model of the primary carbon metabolism in cyanobacterium Synechococcus elongatus PCC 7942, that allows the identification of a specific function for a particular PGM. The strategy employs multiple parameter estimation runs in high CO2, combined with simulations testing a broad range of kinetic parameters against the changes in transcript levels of annotated PGMs. Simulations are evaluated for a match in metabolic level in low CO2, to reveal trends that can be linked to the function of a particular PGM. A one-isoenzyme scenario shows that PGM2 is a major regulator of glycolysis, while PGM1 and PGM4 make the system robust against environmental changes. Strikingly, combining two PGMs with reverse transcriptional regulation allows both features. A conclusion arising from our analysis is that a two-enzyme PGM system is required to regulate the flux between glycolysis and the Calvin-Benson cycle, while an additional PGM increases the robustness of the system.

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Section: Methodsmentioning

confidence: 99%

Phosphoglycerate Mutases Function as Reverse Regulated Isoenzymes in Synechococcus elongatus PCC 7942

Jablonský

Hagemann²,

Schwarz³

2013

PLoS ONE

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“…Our preliminary study showed that a combination of genome-scale and kinetic models improves the model accuracy by implementing minor sink reactions for adjacent pathways [8]. However, the problem of unconstrained parameter estimation remains.…”

Section: Introductionmentioning

confidence: 97%

Multi-Level Kinetic Model Explaining Diverse Roles of Isozymes in Prokaryotes

2014

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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.

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“…There are also many other models for the Calvin cycle in the literature and it would be desirable to do a careful mathematical study of their solutions. This is particularly relevant since several errors in the literature have been discovered which had gone uncorrected for many years [6], [2].…”

Section: Discussionmentioning

confidence: 99%

Overload breakdown in models for photosynthesis

Mohring

Rendall

2016

Dynamical Systems

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In many models of the Calvin cycle of photosynthesis it is observed that there are solutions where concentrations of key substances belonging to the cycle tend to zero at late times, a phenomenon known as overload breakdown. In this paper we prove theorems about the existence and non-existence of solutions of this type and obtain information on which concentrations tend to zero when overload breakdown occurs. As a starting point we take a model of Pettersson and Ryde-Pettersson which seems to be prone to overload breakdown and a modification of it due to Poolman which was intended to avoid this effect.

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Modeling the Calvin-Benson cycle

Cited by 37 publications

References 31 publications

Phosphoglycerate Mutases Function as Reverse Regulated Isoenzymes in Synechococcus elongatus PCC 7942

Phosphoglycerate Mutases Function as Reverse Regulated Isoenzymes in Synechococcus elongatus PCC 7942

Multi-Level Kinetic Model Explaining Diverse Roles of Isozymes in Prokaryotes

Overload breakdown in models for photosynthesis

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