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notes: This a model from the article: A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast. Schaber J, Kofahl B, Kowald A, Klipp E FEBS J. 2006 Aug; 273(15):3520-33 16884493 , Abstract: Cells must be able to process multiple information in parallel and, moreover, they must also be able to combine this information in order to trigger the appropriate response. This is achieved by wiring signalling pathways such that they can interact with each other, a phenomenon often called crosstalk. In this study, we employ mathematical modelling techniques to analyse dynamic mechanisms and measures of crosstalk. We present a dynamic mathematical model that compiles current knowledge about the wiring of the pheromone pathway and the filamentous growth pathway in yeast. We consider the main dynamic features and the interconnections between the two pathways in order to study dynamic crosstalk between these two pathways in haploid cells. We introduce two new measures of dynamic crosstalk, the intrinsic specificity and the extrinsic specificity. These two measures incorporate the combined signal of several stimuli being present simultaneously and seem to be more stable than previous measures. When both pathways are responsive and stimulated, the model predicts that (a) the filamentous growth pathway amplifies the response of the pheromone pathway, and (b) the pheromone pathway inhibits the response of filamentous growth pathway in terms of mitogen activated protein kinase activity and transcriptional activity, respectively. Among several mechanisms we identified leakage of activated Ste11 as the most influential source of crosstalk. Moreover, we propose new experiments and predict their outcomes in order to test hypotheses about the mechanisms of crosstalk between the two pathways. Studying signals that are transmitted in parallel gives us new insights about how pathways and signals interact in a dynamical way, e.g., whether the…
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species: metaid_0000064

650956
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000063

metaid_0000036
type: Parameter
constant: true
value: 0.1
name: k15

metaid_0000021
type: Parameter
constant: true
value: 1.0
name: k13

metaid_0000017
type: Parameter
constant: true
value: 1.0
name: k9

metaid_0000082
type: Reaction
is version of: GO:0016310
product: 650737
reversible: true
fast: false
product: 650725
is: SBO:0000216
name: v5
is version of: GO:0043241
reactant: 650713
kinetic law: 650749

650737
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

650725
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000058

650713
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000057

metaid_0000024
type: Parameter
constant: true
value: 1.0
name: k20

metaid_0000100
type: Reaction
is version of: GO:0016310
modifier: 651596
name: v23
reversible: true
reactant: 651572
product: 651584
fast: false
is: SBO:0000216
kinetic law: 651608

651572
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000073

651584
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000074

metaid_0000085
type: Reaction
kinetic law: 650895
product: 650883
reactant: 650871
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: true
name: v8

650883
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000061

650871
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000060

metaid_0000103
type: Reaction
kinetic law: 651740
product: 651728
reactant: 651716
is version of: GO:0016311
is: SBO:0000330
fast: false
reversible: true
name: v26

651728
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000055

651716
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000058

metaid_0000043
type: Parameter
constant: true
value: 0.01
name: k2

metaid_0000039
type: Parameter
constant: true
value: 0.1
name: k30

metaid_0000046
type: Parameter
constant: true
value: 0.01
name: k29

metaid_0000005
type: Parameter
constant: true
value: 1.0
name: alphaA

metaid_0000090
type: Reaction
kinetic law: 651112
product: 651100
reactant: 651088
is version of: GO:0016310
is: SBO:0000216
fast: false
reversible: true
name: v13

651100
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000066

651088
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000051

metaid_0000098
type: Reaction
product: 651500
fast: false
reactant: 651476
reversible: true
name: v21
kinetic law: 651512
is: SBO:0000180
is version of: GO:0043241
product: 651488

651500
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000073

651476
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000072

651488
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

metaid_0000078
type: Reaction
reversible: true
fast: false
is version of: GO:0006461
kinetic law: 650568
product: 650556
reactant: 650544
name: v1
is: SBO:0000177
reactant: 650532

650556
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000052

650544
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000051

650532
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000050

metaid_0000032
type: Parameter
constant: true
value: 1.0
name: k33

metaid_0000012
type: Parameter
constant: true
value: 360.0
name: betae

W3 CDTF: Thu Aug 20 18:18:13 BST 2009

W3 CDTF: Thu Sep 08 12:27:23 BST 2011

ORG:
  orgname: Max Planck Institute for Molecular Genetics, Computational Systems Biology Group, Germany.
n:
  given: Jorg
  family: Schaber

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah