Understanding the impact of the cofactor swapping of isocitrate dehydrogenase over the growth phenotype of Escherichia coli on acetate by using constraint-based modeling
Author
dc.contributor.author
Armingol, Erick
Author
dc.contributor.author
Tobar Almonacid, Eduardo
Author
dc.contributor.author
Cabrera Paucar, Ricardo
Admission date
dc.date.accessioned
2018-08-30T15:31:08Z
Available date
dc.date.available
2018-08-30T15:31:08Z
Publication date
dc.date.issued
2018
Cita de ítem
dc.identifier.citation
PLoS ONE 13(4): e0196182
es_ES
Identifier
dc.identifier.other
10.1371/journal.pone.0196182
Identifier
dc.identifier.uri
https://repositorio.uchile.cl/handle/2250/151385
Abstract
dc.description.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.
es_ES
Patrocinador
dc.description.sponsorship
FONDECYT 1121170 (CONICYT),
Project VID ENL012/16 (Universidad de Chile),
CINV Millennium Institute, and PEEI of Biology
Department (Universidad de Chile)
Understanding the impact of the cofactor swapping of isocitrate dehydrogenase over the growth phenotype of Escherichia coli on acetate by using constraint-based modeling