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Why
do
metabolic
networks
look
like
they
do?
Petter
Holme
Whatis
similar?
Whatis
similar?
Fundamental
constraintsom
physics,chemistry&
biology.
Whatis
similar?
Whatis
different?
Fundamental
constraintsom
physics,chemistry&
biology.
Whatis
similar?
Whatis
different?
Fundamental
constraintsom
physics,chemistry&
biology.
Mechanismsof
evolution&
adaptation.
What do metabolic
networks look like?
What do metabolic
networks look like?
What do metabolic
networks look like?
What is a metabolic
network?
What do metabolic
networks look like?
What is a metabolic
network?
O+O₃→3O₂
2O₂+CH₄→ CO₂+2H₂O
OH⁻
What do metabolic
networks look like?
What is a metabolic
network?
What do metabolic
networks look like?
What is a metabolic
network?
What do metabolic
networks look like?
What is a metabolic
network?
Graphtypes
What do metabolic
networks look like?
What is a metabolic
network?
Representations/ projections
Graphtypes
What do metabolic
networks look like?
What is a metabolic
network?
Currencymetabolites
Representations/ projections
Graphtypes
Complex
Graph types
Simple
Complex
Graph types
Simple
littleinfo,
manymethods
Complex
Graph types
Simple
littleinfo,
manymethods
lots of info,
fewmethods
Representations
2O₂+ CH₄→ CO₂+2H₂O
CH₄
O₂
H₂O
CO₂
Representations
2O₂+ CH₄→ CO₂+2H₂O
CH₄
O₂
H₂O
CO₂
Representations
2O₂+ CH₄→ CO₂+2H₂O
CH₄
O₂
H₂O
CO₂
SUBSTRATE–PRODUCTGRAPH
Representations
2O₂+ CH₄→ CO₂+2H₂O
CH₄
O₂
H₂O
CO₂
SUBSTRATE–SUBSTRATEGRAPH
Representations
2O₂+ CH₄→ CO₂+2H₂O
CH₄
O₂
H₂O
CO₂
SUBSTANCEGRAPH
Hypothesis:Networkclusters~functionalmodules
Holme,Huss,Jeong,2003.Subnetworkhierarchiesof biochemicalpathways,
Bioinformatics19:532–538.
Hypothesis:Networkclusters~functionalmodules
Holme,Huss,Jeong,2003.Subnetworkhierarchiesof biochemicalpathways,
Bioinformatics19:532–538.
Hypothesis:Networkclusters~functionalmodules
Holme,Huss,Jeong,2003.Subnetworkhierarchiesof biochemicalpathways,
Bioinformatics19:532–538.
matchingscore
0.25
0
0.75
0.5
substrate–
product
substrate–
substrate substance
Human(KEGG)
S.cerevisiae(KEGG)
S.cerevisiae(BiGG)
C.elegans
M.musculus
R.norvegicus
D.melanogaster
M.genitalium
E.coli
Human(BiGG)
Matchingnetworkclusters&annotatedfunctions
matchingscore
0.25
0
0.75
0.5
substrate–
product
substrate–
substrate substance
Human(KEGG)
S.cerevisiae(KEGG)
S.cerevisiae(BiGG)
C.elegans
M.musculus
R.norvegicus
D.melanogaster
M.genitalium
E.coli
Human(BiGG)
Holme,Huss,2010.Substancenetworksareoptimalsimple-graph
representationsof metabolism,ChineseSci.Bull.55:3161-3168.
Currencymetabolites
Currencymetabolites
Currencymetabolites
Currencymetabolites
Currencymetabolites
Existsthroughoutthecell
(i.e.manymodules)
Canreactwithagreatvariety
of othersubstances
Currencymetabolites
Existsthroughoutthecell
(i.e.manymodules)
Canreactwithagreatvariety
of othersubstances
Jing,Holme,2010.LectureNotesinOperationsResearch13:13–21.
Currencymetabolites
Existsthroughoutthecell
(i.e.manymodules)
Canreactwithagreatvariety
of othersubstances
lowers the modularity
Currencymetabolites
Existsthroughoutthecell
(i.e.manymodules)
Canreactwithagreatvariety
of othersubstances
lowers the modularity
high degree
Currencymetabolites
Currencymetabolites
Currencymetabolites
Existsthroughoutthecell(i.e.
manymodules)
Canreactwithagreatvariety
of othersubstances
lowers the modularity
high degree
Currencymetabolites
1.calculatemodularity
2.removethevertexwithhighest
degree
3.goto1
edeletedvertexsetwithhighest
modularityarethecurrency
metbolites
Currencymetabolites
0.15
0.14
∆
0.13
0.12
Orthophosphate
Pyrophosphate
CO2
CoA
AMP
NH3
UDP
S–Adenosyl–L–methionine
H2O
H
+
O2
NADPH
NADP
NADH
ATP
NAD
ADP
L–Glutamate
H2O2
deleted vertex number
1 5 10 15
+
+
Currencymetabolites
Wagner,Fell Schuster & al. Ma & Zeng
ATP ATP ATP
ADP ADP ADP
NADP+ NADP+ NADP+
NADPH NADPH
NAD+ NAD+
NADH
Pi Pi
H2O H2O
H+
PPi
CMP CO2
O2
NH3
Currencymetabolites
Wagner,Fell Schuster & al. Ma & Zeng
ATP ATP ATP
ADP ADP ADP
NADP+ NADP+ NADP+
NADPH NADPH
NAD+ NAD+
NADH
Pi Pi
H2O H2O
H+
PPi
CMP CO2
O2
NH3
Huss,Holme,2007.Currencyandcommodity
metabolites,IETSystemsBiology1:280–285.
So what do metabolic
networks look like?
So what do metabolic
networks look like?
Broaddegreedistributions
0.1
10 –2
10 –3
10 –4
10 –5
10 –6
10
3
100101
p(k)
degree,k
So what do metabolic
networks look like?
Broaddegreedistributions
Core-peripherystructure+
aweak butsignificant
modularstructure
So what do metabolic
networks look like?
Broaddegreedistributions
Core-peripherystructure+
aweak butsignificant
modularstructure
So what do metabolic
networks look like?
Broaddegreedistributions
Core-peripherystructure+
aweak butsignificant
modularstructure
So what do metabolic
networks look like?
Broaddegreedistributions
Core-peripherystructure+
aweak butsignificant
modularstructure
Networkmodules~
subcellularlocalization
N
S
H O2
pyruvate, CO2
H O2
CO2
ATP, ADP
pyrophosphate
NADPH, NADH
substrate
reaction node
link
in−flow
out−flow
−D−ribose 1−phosphate
CoA
orthophosphate
adenine
deoxyadenosine
inosine
adenosine
hypoxanthine
guanine
guanosine
deoxyguanosine
D−glucosamine 1−phosphate
1−phosphate
−acetyl−D−glucosamine
acetyl−CoA
dihydrolipoamide
−D−ribose 1−pyrophosphate
−acetyldihydrolipoamide
pyrophosphate
2−deoxy−D−ribose 1−phosphate
iiiiii
Compared to what?
Compared to what?
eproblemof null-models
Compared to what?
eproblemof null-models
Rewired networksviolate
massbalance
Compared to what?
eproblemof null-models
Rewired networksviolate
massbalance
Otherreactionsystems
Compared to what?
Compared to what?
Holme,Huss,Lee,2011.Atmosphericreactionsystemsasnull-modelstoidentifystructuraltraces
of evolutioninmetabolism,PLoSONE6:e19759.
0.1
0.2
0.3
0.4
0.5
0.6
10
3
100 10
3
100 10
40
2
3
4
5
6
1
7
numberof vertices,N numberof edges,M
relativemodularity,∆
numberofcurrencyvertices,c
0
planets
organisms
Finally:Why?
Is theweakmodularity
related torobustness?
Finally:Why?
3.3
3.4
3.5
3.6
3.7
3.8
0.70 0.75 0.80 0.85
modularity
robustness
1.27
1.29
1.31
1.33
1.35
1.37
0.70 0.75 0.80 0.85
robustness
modularity
genetic perturbations chemical perturbations
x!
MikaelHuss
JingZhao
SangHoonLee
x!
MikaelHuss
JingZhao
SangHoonLee
Compared to what?
Holme,2009.Modelvalidationof simple-graph
representationsof metabolism.JRoySocInterface40:1027–1034.
Compared to what?
Holme,2009.Modelvalidationof simple-graph
representationsof metabolism.JRoySocInterface40:1027–1034.
Compared to what?
Holme,2009.Modelvalidationof simple-graph
representationsof metabolism.JRoySocInterface40:1027–1034.

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Why do metabolic networks look like they do?