Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks
Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a revie...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
MDPI AG
2009-04-01
|
Series: | International Journal of Molecular Sciences |
Subjects: | |
Online Access: | http://www.mdpi.com/1422-0067/10/4/1697/ |
id |
doaj-be47fdb9e93543a3b3b6f10cc3bfd9b4 |
---|---|
record_format |
Article |
spelling |
doaj-be47fdb9e93543a3b3b6f10cc3bfd9b42020-11-25T00:34:25ZengMDPI AGInternational Journal of Molecular Sciences1422-00672009-04-011041697171810.3390/ijms10041697Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer NetworksMarko VendelinPearu PetersonToomas PaalmeDavid W. SchryerIsotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prerequisite for the intelligent design of genetically modified organisms able to realize their potential of revolutionizing food, energy, and pharmaceutical production. We describe techniques to explore the bidirectionality and compartmentalization of metabolic fluxes using information contained in the isotopic transient, and discuss the integration of kinetic models with MFA. The flux parameters of an example metabolic network were optimized to examine the compartmentalization of metabolites and and the bidirectionality of fluxes in the TCA cycle of Saccharomyces uvarum for steady-state respiratory growth. http://www.mdpi.com/1422-0067/10/4/1697/Metabolic networkisotopomer dynamicsMFAmathematical modelingcompartmentalization¹³C NMR |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Marko Vendelin Pearu Peterson Toomas Paalme David W. Schryer |
spellingShingle |
Marko Vendelin Pearu Peterson Toomas Paalme David W. Schryer Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks International Journal of Molecular Sciences Metabolic network isotopomer dynamics MFA mathematical modeling compartmentalization ¹³C NMR |
author_facet |
Marko Vendelin Pearu Peterson Toomas Paalme David W. Schryer |
author_sort |
Marko Vendelin |
title |
Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks |
title_short |
Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks |
title_full |
Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks |
title_fullStr |
Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks |
title_full_unstemmed |
Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks |
title_sort |
bidirectionality and compartmentation of metabolic fluxes are revealed in the dynamics of isotopomer networks |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2009-04-01 |
description |
Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prerequisite for the intelligent design of genetically modified organisms able to realize their potential of revolutionizing food, energy, and pharmaceutical production. We describe techniques to explore the bidirectionality and compartmentalization of metabolic fluxes using information contained in the isotopic transient, and discuss the integration of kinetic models with MFA. The flux parameters of an example metabolic network were optimized to examine the compartmentalization of metabolites and and the bidirectionality of fluxes in the TCA cycle of Saccharomyces uvarum for steady-state respiratory growth. |
topic |
Metabolic network isotopomer dynamics MFA mathematical modeling compartmentalization ¹³C NMR |
url |
http://www.mdpi.com/1422-0067/10/4/1697/ |
work_keys_str_mv |
AT markovendelin bidirectionalityandcompartmentationofmetabolicfluxesarerevealedinthedynamicsofisotopomernetworks AT pearupeterson bidirectionalityandcompartmentationofmetabolicfluxesarerevealedinthedynamicsofisotopomernetworks AT toomaspaalme bidirectionalityandcompartmentationofmetabolicfluxesarerevealedinthedynamicsofisotopomernetworks AT davidwschryer bidirectionalityandcompartmentationofmetabolicfluxesarerevealedinthedynamicsofisotopomernetworks |
_version_ |
1725313397196587008 |