Creating and Analysing a Metabolic Network for Malaria
www.tomforth.co.uk
Tom Forth
Wikipedia - a topic for discussion
Status of Biological Network and Modelling pages on Englishlanguage wikipedia.
•
KEGG – stub
•
MetaCyc – stub
•
EcoCyc – stub
•
Fluxomics – no page
•
ChEBI – stub
•
Flux Balance Analysis – stub (mid-2010)
•
Dynamic FBA – no page
•
SBML – strong article (Hucka & LeNov)
•
SBGN – strong article (Hucka & LeNov)
Principles of Flux-Balance Analysis
‘flux balance analysis’ on wikipedia
Principles of Flux-Balance Analysis
Increased x4 since rewrite (x3 normalised)
The first six reactions in Glycolysis prepared for FBA through the
addition of an objective function (red) and the import and export
of nutrients (ATP, ADP, BDG, ADG) across the system boundary
(dashed green line)
The results of FBA on a prepared metabolic network of the top
six reactions of glycolysis. The predicted flux through each
reaction is proportional to the width of the line. Objective
function in red, constraints on alpha-D-Glucose and beta-DGlucose import represented as red bars.
An example of a non lethal gene deletion in a
sample metabolic network with fluxes shown
by the weight of the reaction lines as
calculated by FBA. Here the flux through the
objective function is halved but is still
present.
An example of a lethal gene deletion in a
sample metabolic network with fluxes shown
by the weight of the reaction lines as
calculated by FBA. Here there is no flux
through the objective function, simulating that
the pathway is no longer functional.
Creating a Network
Forth, T., McConkey, G. A, & Westhead, D. R. (2010). MetNetMaker: A free and open-source tool
for the creation of novel metabolic networks in SBML format. Bioinformatics (Oxford, England),
2-3. doi: 10.1093/bioinformatics/btq425.
www.metnetmaker.com
Reaction Id
Oxaloacetate_
Pyruvate_cto
aCoa_ctoa
PEP_ctoa
H_btoc
NADH_btoc
ATP_btoc
ADP_btoc
NADP_btoc
NADPH_btoc
H2O_btoc
FADH2_btoc
FAD_btoc
CO2_btoc
GDP_btoc
GTP_btoc
Glycerol_btoc
ADG_btoc
BDG_btoc
Slactate_btoc
R00768
R02058
R02086
R00415
R01007
R04216
R01787
R01600
R01786
R02739
R02740
R03321
R04779
R01070
R01061
R01512
Compartment
Special
Transfer
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Special
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
Cytosol
EC Number
spontaneous
unknown
spontaneous
unknown
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
spontaneous
2.6.1.16
2.3.1.4
unknown
unknown
2.7.8.15
2.4.1.119
1.1.1.21
2.7.1.1
2.7.1.1
5.3.1.9
5.3.1.9
5.3.1.9
2.7.1.11
4.1.2.13
1.2.1.12
2.7.2.3
Max +ve Flux
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
500
Max -ve Flux
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
-500
Objective
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
Map Number
00620
00530
00530
00530
00530
00530
00530
00010
00010
00010
00010
00010
00010
00010
00010
00010
00010
Gene
Rev
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
TRUE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
TRUE
Notes
Visualising the Network
Huthmacher C, Hoppe A, Bulik S, Holzhutter H-G. Antimalarial
drug targets in Plasmodium falciparum predicted by stagespecific metabolic network analysis. BMC Systems Biology.
2010;4(1):120. Available at:
http://www.biomedcentral.com/1752-0509/4/120 [Accessed
September 1, 2010].
Huthmacher C, Hoppe A, Bulik S, Holzhutter
H-G. Antimalarial drug targets in
Plasmodium falciparum predicted by stagespecific metabolic network analysis. BMC
Systems Biology. 2010;4(1):120. Available
at: http://www.biomedcentral.com/17520509/4/120 [Accessed September 1, 2010].
Plata G, Hsiao T-L, Olszewski KL, Llinás M,
Vitkup D. Reconstruction and flux-balance
analysis of the Plasmodium falciparum
metabolic network. Molecular Systems Biology.
2010;6(408). Available at:
http://www.nature.com/doifinder/10.1038/ms
b.2010.60 [Accessed September 8, 2010].
1. Ginsburg H. Progress in in silico
functional genomics: the malaria
Metabolic Pathways database.
Trends in parasitology.
2006;22(6):238-40. Available at:
http://www.ncbi.nlm.nih.gov/pubm
ed/16707276.
Glycolysis
Pentose Phosphate Cycle
Pyruvate Metabolism
Glycolysis
Pentose Phosphate Cycle
Pyruvate Metabolism
Glyoxylate Metabolism
Fructose Metabolism
Mannose Metabolism
TCA Cycle
Carbohydrate Metabolism
Nucleotide Metabolism
Carbohydrate Metabolism
Nucleotide Metabolism
Lipid Metabolism
Carbohydrate Metabolism
Nucleotide Metabolism
Lipid Metabolism
Amino Acid Metabolism
Projecting predicted fluxes onto the
network
Measuring a Biomass function
Awaiting integration with recently published measurements and metabolic model
Measuring fluxes in the organism
Fresh Media
Media: after having
malaria grown in it
Fresh Media
Media: after having
malaria grown in it
+
+
–
–
–
+
+
0.8
0.6
Glycerol Integral
0.5
0.4
0.3
0.2
0.1
0
0.00
20.00
40.00
60.00
0.00
Hour of Experiment
60.00
0.8
0.7
2
Tyrosine Integral
Isoleucine integral
40.00
Hour of Experiment
2.5
1.5
1
0.5
0.6
0.5
0.4
0.3
0.2
Glutamine (mg/ml)
0.1
0
0
0.00
20.00
40.00
60.00
0.00
Hour of Experiment
20.00
40.00
60.00
Hour of Experiment
1.6
Phenylalanine Integral
2.5
2
Valine Integral
20.00
1.5
1
0.5
0
1.4
1.2
1
0.8
0.6
0.4
0.2
20.00
40.00
Hour of Experiment
60.00
0.4
0.4
0.3
0.3
0.3
0.3
0.3
0.2
0
0
0.00
Metabolite Concentration in Media
(mg/ml)
Alanine Inegral
0.7
4.5
4
3.5
3
2.5
2
1.5
1
0.5
0
0.00
20.00
40.00
Hour of Experiment
60.00
10
20
30
40
Experiment Time (hours)
50
Bringing it all together in a visualised model
In Summary
• Why aren’t we using the most-read resource to share our
knowledge?
• MetNetMaker was my understanding, as an outsider, of the way
forward at the time and has been reasonably successful. It has been
published, widely downloaded and is now used both in Academia
and Business. My mistakes are likely to be widespread, I’m happy to
share them.
• 3 metabolic network for P. falciparum now exist. SBML helps, but
their ontologies are largely incompatible.
• Findings from P. falciparum models are not yet understandable by
Biologists. Visualisation may help a little bit but we must do better.
Links and Thanks
Prof. David Westhead
Dr. Glenn McConkey
The White Rose DTC
Jenny Lake
Cassey McRae
Prof. Julie Fisher
www.tomforth.co.uk
www.metnetmaker.com
‘Flux Balance Analysis’ on Wikipedia