A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana
Catherine
Lloyd
Auckland Bioengineering Institute, The University of Auckland
Model Status
This model contains no ODEs and as such can not currently be solved by any of the available CellML tools. However the model is known to be valid CellML and the units are consistent. Also the CellML model appears to match the published equations.
Model Structure
ABSTRACT: This work proposes a model of the metabolic branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana which involves kinetic competition for phosphohomoserine between the allosteric enzyme threonine synthase and the two-substrate enzyme cystathionine gamma-synthase. Threonine synthase is activated by S-adenosylmethionine and inhibited by AMP. Cystathionine gamma-synthase condenses phosphohomoserine to cysteine via a ping-pong mechanism. Reactions are irreversible and inhibited by inorganic phosphate. The modelling procedure included an examination of the kinetic links, the determination of the operating conditions in chloroplasts and the establishment of a computer model using the enzyme rate equations. To test the model, the branch-point was reconstituted with purified enzymes. The computer model showed a partial agreement with the in vitro results. The model was subsequently improved and was then found consistent with flux partition in vitro and in vivo. Under near physiological conditions, S-adenosylmethionine, but not AMP, modulates the partition of a steady-state flux of phosphohomoserine. The computer model indicates a high sensitivity of cystathionine flux to enzyme and S-adenosylmethionine concentrations. Cystathionine flux is sensitive to modulation of threonine flux whereas the reverse is not true. The cystathionine gamma-synthase kinetic mechanism favours a low sensitivity of the fluxes to cysteine. Though sensitivity to inorganic phosphate is low, its concentration conditions the dynamics of the system. Threonine synthase and cystathionine gamma-synthase display similar kinetic efficiencies in the metabolic context considered and are first-order for the phosphohomoserine substrate. Under these conditions outflows are coordinated.
The original paper reference is cited below:
A Kinetic Model of the Branch-Point between the Methionine and Threonine Biosynthesis Pathways in Arabidopsis thaliana
, Gilles Curien, Stephane Ravanel and Renaud Dumas, 2003,
European Journal of Biochemistry
, 270, 4615-4627. PubMed ID: 14622248
reaction diagram
Schematic diagram of the Phser branch-point in the aspartate-derived amino acid biosynthetic pathway in plants.
$\mathrm{v\_cystathionine}=\frac{\mathrm{kcat\_CGS\_app\_Cys}\mathrm{CGS}\mathrm{Cys}}{\mathrm{Km\_CGS\_app\_Cys}+\mathrm{Cys}}\mathrm{kcat\_CGS\_app\_Cys}=\frac{\mathrm{kcat\_CGS}}{1.0+\frac{\mathrm{Km\_CGS\_Phser}}{\mathrm{Phser}}(1.0+\frac{\mathrm{Pi}}{\mathrm{Ki\_CGS\_Pi}})}\mathrm{Km\_CGS\_app\_Cys}=\frac{\mathrm{Km\_CGS\_Cys}}{1.0+\frac{\mathrm{Km\_CGS\_Phser}}{\mathrm{Phser}}(1.0+\frac{\mathrm{Pi}}{\mathrm{Ki\_CGS\_Pi}})}$
$\mathrm{v\_Thr}=\frac{\mathrm{TS}\mathrm{kcat\_TS}\mathrm{Phser}}{\mathrm{Km\_TS}+\mathrm{Phser}}\mathrm{kcat\_TS}=\frac{\mathrm{kcat\_TS\_noAdoMet}+\mathrm{kcat\_TS\_AdoMet}\frac{\mathrm{AdoMet}^{2.0}}{\mathrm{K1K2}}}{1.0+\frac{\mathrm{AdoMet}^{2.0}}{\mathrm{K1K2}}}\mathrm{Km\_TS}=\frac{250.0\frac{1.0+\frac{\mathrm{AdoMet}}{0.5}}{1.0+\frac{\mathrm{AdoMet}}{1.1}}}{1.0+\frac{\mathrm{AdoMet}^{2.0}}{140.0}}(1.0+\frac{\mathrm{Pi}}{\mathrm{Ki\_TS\_Pi}})$
$\mathrm{J\_Phser}=\mathrm{v\_cystathionine}+\mathrm{v\_Thr}$
CGS
cystathionine gamma-synthase
Phser
phosphohomoserine
AdoMet
S-adenosylmethionine
Cys
cysteine
Pi
inorganic phosphate
TS
threonine synthase
A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana
270
4615
4627
Stephane
Ravanel
Curien et al.'s 2003 kinetic model of the branch-point between
methionine and threonine biosynthesis pathways in Arabidopsis thaliana.
Arabidopsis thaliana
2003-12
The University of Auckland, Auckland Bioengineering Institute
2003-12-22T00:00:00+00:00
c.lloyd@auckland.ac.nz
Renaud
Dumas
The University of Auckland
Auckland Bioengineering Institute
2009-06-08T16:07:15+12:00
Catherine
Lloyd
May
Gilles
Curien
updated curation status,
removed reference link in documentation
14622248
keyword
arabidopsis
metabolism
James
Lawson
Richard
This is the CellML description of Curien et al.'s 2003 kinetic model
of the branch-point between methionine and threonine biosynthesis
pathways in Arabidopsis thaliana.
Catherine Lloyd
European Journal of Biochemistry