LP Solutions and Metabolic Flux Analysis
Compared
David Fell & Mark Poolman
dfell@brookes.ac.uk
http://mudshark.brookes.ac.uk
Edinburgh 2011: - p. 1
The Arabidopsis Model
LP and MFA compared
● The Arabidopsis Model
● Validating the LP Optima
● The LP Analysis
● The MFA Model
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
Summary of the model:
■ Extracted 1646 metabolites and 1742
reactions from the AraCyc annotation.
■ Removed problemmatic, unbalanced or
erroneous reactions, leaving 1231 x 1336.
■ Added transport reactions to give 1253
metabolites and 1406 reactions.
■ Showed the model was able to account for
synthesis of the major biomass precursors.
■ Found that minimal LP solutions accounting
for growth of heterotrophic culture cells on
glucose contain only 232 reactions.
Poolman et al, Plant Physiol 151, 1570-1581 (2009)
Edinburgh 2011: - p. 2
Validating the LP Optima
LP and MFA compared
● The Arabidopsis Model
● Validating the LP Optima
● The LP Analysis
■
How close are predicted optimal solutions to the actual flux
distributions?
● The MFA Model
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
Edinburgh 2011: - p. 3
Validating the LP Optima
LP and MFA compared
■
● The Arabidopsis Model
● Validating the LP Optima
● The LP Analysis
● The MFA Model
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
■
How close are predicted optimal solutions to the actual flux
distributions?
13
C Metabolic Flux Analysis has been carried out by our
collaborators on the same Arabidopsis cell culture in both
control conditions and in cells subject to osmotic and heat
stress. The MFA metabolic model is less detailed, but
equivalences can be found in central metabolism between it
and the LP model.
Edinburgh 2011: - p. 3
Validating the LP Optima
LP and MFA compared
■
● The Arabidopsis Model
● Validating the LP Optima
● The LP Analysis
● The MFA Model
● The MFA Model
■
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
■
How close are predicted optimal solutions to the actual flux
distributions?
13
C Metabolic Flux Analysis has been carried out by our
collaborators on the same Arabidopsis cell culture in both
control conditions and in cells subject to osmotic and heat
stress. The MFA metabolic model is less detailed, but
equivalences can be found in central metabolism between it
and the LP model.
We carried out LP calculations for the glucose consumption,
growth rate and biomass composition measured for each of
the experimental conditions and compared it with the
equivalent fluxes in the MFA solutions.
Edinburgh 2011: - p. 3
The LP Analysis
LP and MFA compared
● The Arabidopsis Model
● Validating the LP Optima
■
The LP solutions for the minimum fluxes accounting for
biomass and growth rate require much less glucose uptake
than that observed in all conditions.
■
We know the cells convert glucose only to biomass and CO2 .
We presume the additional glucose consumption is partly for
polymerisation costs, but mainly for maintenance energy and
polymer turnover.
■
Representing the maintenance energy as additional ATPase
flux, we scan ATPase activity until the LP solution for glucose
consumption matches the observed.
● The LP Analysis
● The MFA Model
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
Edinburgh 2011: - p. 4
The MFA Model
Cytosol
pentose cell wall
hexose cell wall
pcellwall
hcellwall
LP and MFA compared
Plastid
starch
cpex
upt
glucose
starch
CO2in
phexose-phosphate
chexose-phosphate
● The Arabidopsis Model
ssucGOUT
● Validating the LP Optima
ppp1
sucrose
● The LP Analysis
his
● The MFA Model
chex2
phex1
● Relative Flux Changes:
Osmotic Stress
ser
Asp
OAA
Ala
ana3
cpyruvate
malate
tca1
tca2
CO2in
cit
scit
cit
lip2
tca5a+b
ssucc
Asp
tca3
Leu
leu2
Lys
lys1a
ile
lys1b
Asn
asn
Gln
tca4a+b αKG
Asp
gln
sfumOUT
glu
Glu
CO2in
Mitochondrion
Ile
CO2in
CO2in
arg
fum
CO2int
CO2in
fattyacids
succinate
Val
leu1
pAcCoA
CO2in
val
ppyruvate
lip1
mpyruvate
CO2in
tyr Tyr
phex2
cmex
OAA
chorismate
chor
chex3
ala
phe
Phe
ana1
fumarate
gly Gly
phosphoenolpyruvate
Summary
smal
Ser
cphex
CO2in
asp
ppp2ppp5
cys Cys
glyceraldehyde 3-phosphate
ana3
PPP
ppp4+ppp5
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
His
CO2in
pro
Pro
thr
met
Thr
Met
arg
gaba
GABA
CO2in
Arg
Edinburgh 2011: - p. 5
The MFA Model
100
LP and MFA compared
● Validating the LP Optima
● The LP Analysis
● The MFA Model
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
Log fluxes (mmol d-1 L culture-1)
from genome-scale model
● The Arabidopsis Model
10
1
0.1
0.01
0.001
0.001
0.01
0.1
1
10
100
Log Fluxes (mmol d-1 L culture-1) from MFA
Edinburgh 2011: - p. 6
Comparison of the LP and MFA Solutions
LP and MFA compared
● The Arabidopsis Model
● Validating the LP Optima
● The LP Analysis
● The MFA Model
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
Edinburgh 2011: - p. 7
Relative Flux Changes: Heat
LP and MFA compared
● The Arabidopsis Model
● Validating the LP Optima
● The LP Analysis
● The MFA Model
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
Williams et al, Plant Physiol. 154, 311–323 (2010)
Edinburgh 2011: - p. 8
Relative Flux Changes: Osmotic Stress
LP and MFA compared
● The Arabidopsis Model
● Validating the LP Optima
● The LP Analysis
● The MFA Model
● The MFA Model
● Comparison of the LP and
MFA Solutions
● Relative Flux Changes: Heat
● Relative Flux Changes:
Osmotic Stress
Summary
Williams et al, Plant Physiol. 154, 311–323 (2010)
Edinburgh 2011: - p. 9
Summary
■
LP flux predictions are similar, but not identical to,
experimentally measured flux distributions.
■
More exploration needed to find whether other constraints
and optimization functions can improve the match.
LP and MFA compared
Summary
● Summary
● Acknowledgements
● Metabolic Pathway Analysis 3
● Acknowledgements — My
Group
Edinburgh 2011: - p. 10
Acknowledgements
LP and MFA compared
Summary
● Summary
● Acknowledgements
● Metabolic Pathway Analysis 3
● Acknowledgements — My
Group
■ Oxford Plant Sciences:
◆
◆
◆
◆
◆
◆
Lee Sweetlove
George Ratcliffe
Laurent Miguet
Andy Howden
Tom Williams
Maurice Cheung
Funding:
Edinburgh 2011: - p. 11
Metabolic Pathway Analysis 3
71st Harden Conference of the Biochemical Society
19—23 September 2011
Chester UK
Edinburgh 2011: - p. 12
Acknowledgements — My Group
LP and MFA compared
Summary
● Summary
● Acknowledgements
● Metabolic Pathway Analysis 3
● Acknowledgements — My
Group
Mark Poolman
Unni Chokkathukalam
Albert Gevorgyan
ScrumPy is available from
http://mudshark.brookes.ac.uk/Software
Edinburgh 2011: - p. 13