Yeast lipid Metabolism model

Model of the lipid metabolism in the yeast Saccharomyces cerevisiae
Written by Vera Schützhold, Jens Hahn - 2015
Written in Python 2.7

Files

Model files

• components: stores multiple component classes for initialisation of lipid objects. Called by reactions.

  • lipids (phospholipids, TAG, CL)
  • fatty acids
  • sterol
  • sterylester
  • sphingolipid

• reactions: reaction class, performs all reactions in one time step. Called by model

  • run_step (permute order of reactions)
  • glycerol 3-p synthesis
  • inositol synthesis
  • ceramide synthesis
  • acetyl-coa synthase
  • acyl synthase
  • PA synthesis
  • lyso PA synthase
  • PA synthase
  • CDP-DG synthase
  • TAG synthesis
  • DAG synthase
  • TAG synthase
  • TAG lipase
  • DAG kinase
  • PS synthase
  • PI synthase
  • PE synthase
  • PC synthase
  • CL synthase
  • ergosterol synthase
  • sterylester synthase
  • sphingolipid synthase
  • transport reaction

• model: model class

  • init (initialise parameters, lists, precursors, molecules and simulation)
  • run (start simulation, return 3 Python dicts - saturation dist., membrane lengths and composition)
  • start (generate initial cell state)
  • cell_cycle (cell cycle tracker)
  • numbers (counts and saves membrane lengths)
  • membrane_compositions (saves membrane compositions)
  • saturation_counter (saves FA saturations)

Examples

• comparison: comparison between stochastic and deterministic MM (supplementary Figure S4)

Simulation

• simulate_print: perform 1000 simulations and save results in csv files
• test_ergosterol: disable ergosterol synthase, perform 1000 simulations and save results in csv files
• test_inositol: increase inositol addition, perform 1000 simulations and save results in csv files

Sensitivity analysis

• rates_SA: change rate of reaction, perform 1000 simulations and save results in csv files This script has to be called with reaction name as argument: e.g.: python rates_SA.py glycerol_3_p_synthesis

Names of reactions and change of rates are shown here, initial values shown in brackets:
glycerol_3_p_synthesis: + 1 (8)
inositol_synthesis: + 1 (5)
ceramide_synthesis: + + 1 (2)
acetyl_coa_synthase: + 65 (650)
acyl_synthase: + 45 (450)
PA_synthesis: + 2 (17)
CDP_DG_synthase: + 2 (20)
TAG_synthesis: + 3 (34)
TAG_lipase: + 2 (23)
DAG_kinase: + 4 (40)
PS_synthase: + 2 (18)
PI_synthase: + 1 (6)
PE_synthase: + 2 (12)
PC_synthase: + 1 (5)
CL_synthase: + 1 (2)
ergosterol_synthase: + 3 (25)
sterylester_synthase: + 3 (27)
sphingolipid_synthase: + 1 (2)