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Understanding the impact of the cofactor swapping of isocitrate dehydrogenase over the growth phenotype of Escherichia coli on acetate by using constraint-based modeling.
PLoS One. 2018; 13(4):e0196182.Plos

Abstract

It has been proposed that NADP+-specificity of isocitrate dehydrogenase (ICDH) evolved as an adaptation of microorganisms to grow on acetate as the sole source of carbon and energy. In Escherichia coli, changing the cofactor specificity of ICDH from NADP+ to NAD+ (cofactor swapping) decreases the growth rate on acetate. However, the metabolic basis of this phenotype has not been analyzed. In this work, we used constraint-based modeling to investigate the effect of the cofactor swapping of ICDH in terms of energy production, response of alternative sources of NADPH, and partitioning of fluxes between ICDH and isocitrate lyase (ICL) -a crucial bifurcation when the bacterium grows on acetate-. We generated E. coli strains expressing NAD+-specific ICDH instead of the native enzyme, and bearing the deletion of the NADPH-producing transhydrogenase PntAB. We measured their growth rate and acetate uptake rate, modeled the distribution of metabolic fluxes by Flux Balance Analysis (FBA), and quantified the specific activities of NADPH-producing dehydrogenases in central pathways. The cofactor swapping of ICDH led to one-third decrease in biomass yield, irrespective of the presence of PntAB. According to our simulations, the diminution in growth rate observed upon cofactor swapping could be explained by one-half decrease in the total production of NADPH and a lower availability of carbon for biosynthesis because of a change in the partition at the isocitrate bifurcation. Together with an increased total ATP production, this scenario resulted in a 10-fold increment in the flux of ATP not used for growing purposes. PntAB was identified as the primary NADPH balancing response, with the dehydrogenases of the oxidative branch of the Pentose Phosphate Pathway and the malic enzyme playing a role in its absence. We propose that in the context of E. coli growing on acetate, the NADP+-specificity of ICDH is a trait that impacts not only NADPH production, but also the efficient allocation of carbon and energy.

Authors+Show Affiliations

Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

29677222

Citation

Armingol, Erick, et al. "Understanding the Impact of the Cofactor Swapping of Isocitrate Dehydrogenase Over the Growth Phenotype of Escherichia Coli On Acetate By Using Constraint-based Modeling." PloS One, vol. 13, no. 4, 2018, pp. e0196182.
Armingol E, Tobar E, Cabrera R. Understanding the impact of the cofactor swapping of isocitrate dehydrogenase over the growth phenotype of Escherichia coli on acetate by using constraint-based modeling. PLoS One. 2018;13(4):e0196182.
Armingol, E., Tobar, E., & Cabrera, R. (2018). Understanding the impact of the cofactor swapping of isocitrate dehydrogenase over the growth phenotype of Escherichia coli on acetate by using constraint-based modeling. PloS One, 13(4), e0196182. https://doi.org/10.1371/journal.pone.0196182
Armingol E, Tobar E, Cabrera R. Understanding the Impact of the Cofactor Swapping of Isocitrate Dehydrogenase Over the Growth Phenotype of Escherichia Coli On Acetate By Using Constraint-based Modeling. PLoS One. 2018;13(4):e0196182. PubMed PMID: 29677222.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Understanding the impact of the cofactor swapping of isocitrate dehydrogenase over the growth phenotype of Escherichia coli on acetate by using constraint-based modeling. AU - Armingol,Erick, AU - Tobar,Eduardo, AU - Cabrera,Ricardo, Y1 - 2018/04/20/ PY - 2018/01/22/received PY - 2018/04/06/accepted PY - 2018/4/21/entrez PY - 2018/4/21/pubmed PY - 2018/7/24/medline SP - e0196182 EP - e0196182 JF - PloS one JO - PLoS One VL - 13 IS - 4 N2 - It has been proposed that NADP+-specificity of isocitrate dehydrogenase (ICDH) evolved as an adaptation of microorganisms to grow on acetate as the sole source of carbon and energy. In Escherichia coli, changing the cofactor specificity of ICDH from NADP+ to NAD+ (cofactor swapping) decreases the growth rate on acetate. However, the metabolic basis of this phenotype has not been analyzed. In this work, we used constraint-based modeling to investigate the effect of the cofactor swapping of ICDH in terms of energy production, response of alternative sources of NADPH, and partitioning of fluxes between ICDH and isocitrate lyase (ICL) -a crucial bifurcation when the bacterium grows on acetate-. We generated E. coli strains expressing NAD+-specific ICDH instead of the native enzyme, and bearing the deletion of the NADPH-producing transhydrogenase PntAB. We measured their growth rate and acetate uptake rate, modeled the distribution of metabolic fluxes by Flux Balance Analysis (FBA), and quantified the specific activities of NADPH-producing dehydrogenases in central pathways. The cofactor swapping of ICDH led to one-third decrease in biomass yield, irrespective of the presence of PntAB. According to our simulations, the diminution in growth rate observed upon cofactor swapping could be explained by one-half decrease in the total production of NADPH and a lower availability of carbon for biosynthesis because of a change in the partition at the isocitrate bifurcation. Together with an increased total ATP production, this scenario resulted in a 10-fold increment in the flux of ATP not used for growing purposes. PntAB was identified as the primary NADPH balancing response, with the dehydrogenases of the oxidative branch of the Pentose Phosphate Pathway and the malic enzyme playing a role in its absence. We propose that in the context of E. coli growing on acetate, the NADP+-specificity of ICDH is a trait that impacts not only NADPH production, but also the efficient allocation of carbon and energy. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/29677222/Understanding_the_impact_of_the_cofactor_swapping_of_isocitrate_dehydrogenase_over_the_growth_phenotype_of_Escherichia_coli_on_acetate_by_using_constraint_based_modeling_ L2 - https://dx.plos.org/10.1371/journal.pone.0196182 DB - PRIME DP - Unbound Medicine ER -