Metabolic Oscillations in Saccharomyces cerevisiae
Catherine
Lloyd
Auckland Bioengineering Institute, The University of Auckland
Model Status
This model runs to reproduce published results in COR, OpenCell and PCEnv. The units are consistent throughout. This model currently reproduces Figure 2B, changing KH (to infinity) and f2 (to 1) will allow the model to reproduce Figure 2A. The initial conditions were estimated and the model run to steady state to yield precise values, changing any parameters will necessitate repeating this procedure.
Model Structure
ABSTRACT: Autonomous metabolic oscillations were observed in aerobic continuous culture of Saccharomyces cerevisiae. Experimental investigation of the underlying mechanism revealed that several pathways and regulatory couplings are involved. Here a hypothetical mechanism including the sulfate assimilation pathway, ethanol degradation and respiration is transformed into a mathematical model. Simulations confirm the ability of the model to produce limit cycle oscillations which reproduce most of the characteristic features of the system
The original paper reference is cited below:
Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae, Jana Wolf, Ho-Yong Sohn, Reinhart Heinrich and Hiroshi Kuriyama, 2001, FEBS Letters, 499, 230-234. PubMed ID: 11423122
schematic diagram
Reaction scheme of the model. The following abbreviations are introduced for the metabolites: sul: sulphate ions, aps: adenylyl sulfate, pap: 3-phosphoadenylyl sulfate, hyd: hydrogen sulphide, cys: cysteine, eth: ethanol, aco: acetyl-CoA, S1 and S2: intermediates of the citric acid cycle, oxy: oxygen, C1 and C2: protein complexes involved in oxidative phosphorylation, A3: ATP, A2: ADP, N1: NAD(P)+, N2: NAD(P)H, oah: O-acetylhomoserine. The cytosolic and mitochondrial compartments are characterized by the superscripts c and m, respectively.
sulfate ions
sul
Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisae
499
230
234
total mitochondrial adenosine phosphates
A_m
total cytosolic adenosine phosphates
A_c
oxygen
oxy
total intermediates of the citrate acid cycle
S
cysteine
cys
Ho-Yong
Sohn
The University of Auckland, Auckland Bioengineering Institute
intermediate of the citrate acid cycle
S1
2007-05-31T00:00:00+00:00
NADH
N2
FEBS
3-phosphoadenylyl sulfate
pap
2001-06-22
Jana
Wolf
O-acetylhomoserine
oah
cytosolic ATP
A3_c
mitochondrial ATP
A3_m
Catherine Lloyd
adenylyl sulfate
aps
keyword
metabolic oscillations
metabolism
yeast
c.lloyd@auckland.ac.nz
A dynamic model of metabolic oscillations in yeast
Saccharomyces cerevisae
Catherine
Lloyd
May
Reinhart
Heinrich
The University of Auckland
Auckland Bioengineering Institute
acetyl-CoA
aco
hydrogen sulphide
hyd
11423122
This is the CellML description of Wolf et al's mathematical model of
metabolic oscillations in the yeast Saccharomyces cerevisiae.
Hiroshi
Kuriyama
ethanol
eth