Adams2019 - The regulatory role of shikimate in plant phenylalanine metabolism
Model Identifier
BIOMD0000000847
Short description
This is a mathematical model of phenylalanine metabolism in plants as influenced by shikimate, with specific evidence of how shikimate dynamics influence phenylalanine metabolism as a function of phenylalanine availability.
Format
SBML
(L2V4)
Related Publication
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The regulatory role of shikimate in plant phenylalanine metabolism.
- Adams ZP, Ehlting J, Edwards R
- Journal of theoretical biology , 2/ 2019 , Volume 462 , pages: 158-170 , PubMed ID: 30412698
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany. Electronic address: zachary.adams@mis.mpg.de.
- In higher plants, the amino acid phenylalanine is a substrate of both primary and secondary metabolic pathways. The primary pathway that consumes phenylalanine, protein biosynthesis, is essential for the viability of all cells. Meanwhile, the secondary pathways are not necessary for the survival of individual cells, but benefit of the plant as a whole. Here we focus on the monolignol pathway, a secondary metabolic pathway in the cytosol that rapidly consumes phenylalanine to produce the precursors of lignin during wood formation. In planta monolignol biosynthesis involves a series of seemingly redundant steps wherein shikimate, a precursor of phenylalanine synthesized in the plastid, is transiently ligated to the main substrate of the pathway. However, shikimate is not catalytically involved in the reactions of the monolignol pathway, and is only needed for pathway enzymes to recognize their main substrates. After some steps the shikimate moiety is removed unaltered, and the main substrate continues along the pathway. It has been suggested that this portion of the monolignol pathway fulfills a regulatory role in the following way. Low phenylalanine concentrations (viz. availability) correlate with low shikimate concentrations. When shikimate concentratios are low, flux into the monolignol pathway will be limited by means of the steps requiring shikimate. Thus, when the concentration of phenylalanine is low it will be reserved for protein biosynthesis. Here we employ a theoretical approach to test this hypothesis. Simplified versions of plant phenylalanine metabolism are modelled as systems of ordinary differential equations. Our analysis shows that the seemingly redundant steps can be sufficient for the prioritization of protein biosynthesis over the monolignol pathway when the availability of phenylalanine is low, depending on system parameters. Thus, the phenylalanine precursor shikimate may signal low phenylalanine availability to secondary pathways. Because our models have been abstracted from plant phenylalanine metabolism, this mechanism of metabolic signalling, which we call the Precursor Shutoff Valve (PSV), may also be present in other biochemical networks comprised of two pathways that share a common substrate.
Contributors
Submitter of the first revision: Johannes Meyer
Submitter of this revision: Johannes Meyer
Modellers: Johannes Meyer
Submitter of this revision: Johannes Meyer
Modellers: Johannes Meyer
Metadata information
Curation status
Curated
Modelling approach(es)
Tags
Connected external resources
SBGN view in Newt Editor
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| Adams2019.xml | SBML L2V4 Representation of Adams2019 - The regulatory role of shikimate in plant phenylalanine metabolism | 37.70 KB | Preview | Download |
Additional files |
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| Adams2019.cps | COPASI file of Adams2019 - The regulatory role of shikimate in plant phenylalanine metabolism | 69.66 KB | Preview | Download |
| Adams2019.sedml | SED-ML file of Adams2019 - The regulatory role of shikimate in plant phenylalanine metabolism | 13.71 KB | Preview | Download |
- Model originally submitted by : Johannes Meyer
- Submitted: Nov 10, 2019 8:58:13 PM
- Last Modified: Nov 10, 2019 8:58:13 PM
Revisions
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Version: 4
- Submitted on: Nov 10, 2019 8:58:13 PM
- Submitted by: Johannes Meyer
- With comment: Automatically added model identifier BIOMD0000000847
Legends
: Variable used inside SBML models
: Variable used inside SBML models
Species
| Species | Initial Concentration/Amount |
|---|---|
| X 3 shikimate ; cytosol |
0.0 item |
| X 2 phenylalanine |
0.0 item |
| X 4 CHEBI:91005 |
0.0 item |
| X 1 shikimate ; GO:0009536 |
0.0 item |
Reactions
| Reactions | Rate | Parameters |
|---|---|---|
| X_4 => X_3 | compartment*a_4*X_4/(K_4+X_4) | K_4 = 1.0; a_4 = 75.0 |
| X_2 + X_3 => X_4 | compartment*a_3*X_2*X_3/((K_3_2+X_2)*(K_3_3+X_3)) | K_3_2 = 1.0; K_3_3 = 0.1; a_3 = 75.0 |
| X_1 => X_3 | compartment*(a_2_plus*X_1/(K_2_plus*(1+b2f*X_3)+X_1)-a_2_minus*X_3/(K_2_minus*(1+b2r*X_1)+X_3)) | a_2_minus = 1.5; K_2_minus = 100.0; a_2_plus = 2.0; b2r = 0.0; K_2_plus = 100.0; b2f = 0.0 |
| X_1 => X_2 | compartment*a_1*X_1/(K_1*(1+b*X_2)+X_1) | a_1 = 100.0; b = 1.0; K_1 = 0.1 |
| => X_1 | compartment*a_0 | a_0 = 25.0 |
Curator's comment:
(added: 10 Nov 2019, 20:58:06, updated: 10 Nov 2019, 20:58:06)
(added: 10 Nov 2019, 20:58:06, updated: 10 Nov 2019, 20:58:06)
Reproduced plot of Figure 4(d) in the original publication.
Model simulated and plot produced using COPASI 4.24 (Build 197).