Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli

Modeling metabolism is fundamental for cell factory design. Central carbon metabolism (CCM) is particularly important as it provides the energy and precursors for other biological processes. However, the complex regulation of CCM has not been fully unraveled. Recent studies have shown that CCM is mo...
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Autor*in:	Daniel eMachado [verfasserIn] Markus J Herrgard [verfasserIn] Isabel eRocha [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2015

Schlagwörter:	Allosteric Regulation Escherichia coli Metabolism Systems Biology Constraint-based modeling

Übergeordnetes Werk:	In: Frontiers in Bioengineering and Biotechnology - Frontiers Media S.A., 2014, 3(2015)
Übergeordnetes Werk:	volume:3 ; year:2015

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fbioe.2015.00154

Katalog-ID:	DOAJ066269679

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callnumber-first	T - Technology
author	Daniel eMachado
spellingShingle	Daniel eMachado misc TP248.13-248.65 misc Allosteric Regulation misc Escherichia coli misc Metabolism misc Systems Biology misc Constraint-based modeling misc Biotechnology Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli
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topic_title	TP248.13-248.65 Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli Allosteric Regulation Escherichia coli Metabolism Systems Biology Constraint-based modeling
topic	misc TP248.13-248.65 misc Allosteric Regulation misc Escherichia coli misc Metabolism misc Systems Biology misc Constraint-based modeling misc Biotechnology
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title	Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli
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title_full	Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli
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title_sort	modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of e. coli
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title_auth	Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli
abstract	Modeling metabolism is fundamental for cell factory design. Central carbon metabolism (CCM) is particularly important as it provides the energy and precursors for other biological processes. However, the complex regulation of CCM has not been fully unraveled. Recent studies have shown that CCM is mostly regulated at post-transcriptional levels. To better understand the role of allosteric regulation in controlling the metabolic phenotype, we expand a CCM model of E. coli with allosteric interactions. This model is used to integrate multi-omics datasets and analyze the coordinated changes in enzyme, metabolite and flux levels. We observe cases where allosteric interactions have a major contribution to the metabolic adjustments. Also, we develop a constraint-based method (arFBA) for simulation of metabolic flux distributions accounting for allosteric interactions. This method is used for systematic prediction of potential allosteric regulation under the given experimental conditions based on experimental flux data. The results reveal the importance of key regulatory metabolites, such as fructose-1,6-bisphosphate, in controlling the metabolic flux. Accounting for allosteric interactions in metabolic reconstructions reveals a hidden topology in metabolic networks, improving our understanding of cellular metabolism and fostering the development of novel simulation methods that account for this type of regulation.
abstractGer	Modeling metabolism is fundamental for cell factory design. Central carbon metabolism (CCM) is particularly important as it provides the energy and precursors for other biological processes. However, the complex regulation of CCM has not been fully unraveled. Recent studies have shown that CCM is mostly regulated at post-transcriptional levels. To better understand the role of allosteric regulation in controlling the metabolic phenotype, we expand a CCM model of E. coli with allosteric interactions. This model is used to integrate multi-omics datasets and analyze the coordinated changes in enzyme, metabolite and flux levels. We observe cases where allosteric interactions have a major contribution to the metabolic adjustments. Also, we develop a constraint-based method (arFBA) for simulation of metabolic flux distributions accounting for allosteric interactions. This method is used for systematic prediction of potential allosteric regulation under the given experimental conditions based on experimental flux data. The results reveal the importance of key regulatory metabolites, such as fructose-1,6-bisphosphate, in controlling the metabolic flux. Accounting for allosteric interactions in metabolic reconstructions reveals a hidden topology in metabolic networks, improving our understanding of cellular metabolism and fostering the development of novel simulation methods that account for this type of regulation.
abstract_unstemmed	Modeling metabolism is fundamental for cell factory design. Central carbon metabolism (CCM) is particularly important as it provides the energy and precursors for other biological processes. However, the complex regulation of CCM has not been fully unraveled. Recent studies have shown that CCM is mostly regulated at post-transcriptional levels. To better understand the role of allosteric regulation in controlling the metabolic phenotype, we expand a CCM model of E. coli with allosteric interactions. This model is used to integrate multi-omics datasets and analyze the coordinated changes in enzyme, metabolite and flux levels. We observe cases where allosteric interactions have a major contribution to the metabolic adjustments. Also, we develop a constraint-based method (arFBA) for simulation of metabolic flux distributions accounting for allosteric interactions. This method is used for systematic prediction of potential allosteric regulation under the given experimental conditions based on experimental flux data. The results reveal the importance of key regulatory metabolites, such as fructose-1,6-bisphosphate, in controlling the metabolic flux. Accounting for allosteric interactions in metabolic reconstructions reveals a hidden topology in metabolic networks, improving our understanding of cellular metabolism and fostering the development of novel simulation methods that account for this type of regulation.
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title_short	Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli
url	https://doi.org/10.3389/fbioe.2015.00154 https://doaj.org/article/73fd36c071c94751b085846820264012 http://journal.frontiersin.org/Journal/10.3389/fbioe.2015.00154/full https://doaj.org/toc/2296-4185
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Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli

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