Exercise Systems amp Synthetic Biotechnology elementary flux mode analysis Todays exercise Update network construction What to do with a metabolic network What are elementary flux modes What knowledge can we gain from elementary mode analysis ID: 760092
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Slide1
Veronique Beckersveronique.beckers@uni-saarland.de
Exercise Systems & Synthetic Biotechnology
elementary flux mode analysis
Slide2Todays exercise
Update network construction
What to do with a metabolic network?
What are elementary flux modes?
What knowledge can we gain from elementary mode analysis?
Processing of flux modes in
matlab®
Slide3Update network construction
Project:5 groups Corynebacterium glutamicumAspergillus nigerSaccharomyces cerevisiaeEscherichia coliPseudomonas putidaNetwork construction:Which pathways?Information required: stoichiometry, reversibility, localization, biomass synthesis requirementsBiomass synthesis: protein composition and precursor demand
substrates:
Glucose
Xylose
Saccharose
Fructose
Glycerin
Lactate
Slide4What are elementary flux modes?
Mode = a
single
independent
pathway
Number
of
modes
=
the
number
of
all
possible
,
independent
flux
distributions
in a steady state
Slide5What knowledge can we gain from elementary mode analysis?
Example network of
E. coli
Most
meaningful values are fluxes of an entire
pathway
that
are
normalized
with
respect
to
a
flux
of
interest
, e.g.
substrate
uptake
Slide6What knowledge can we gain from elementary mode analysis?
Slide7Processing of flux modes in matlab®
http://www.csb.ethz.ch/tools/software/efmtool.html
rformulas
={
' --> A'
'A --> C'
'C --> P + D'
'P --> '
'A --> B'
'B <==> C'
'B --> P'
' <==> B'
'D --> '
};
mnet
=
CalculateFluxModes
(
rformulas
);
Slide8Matlab
principles
Slide9What knowledge can we gain from elementary mode analysis?
Example network of
E. coli
for
i
=1:size(mnet.efms,2)
EFMS(:,i)=mnet.efms(:,i)./mnet.efms($$,i);
end
for
j=size(mnet.efms,2):-1:1
if isnan(EFMS($$,j))==1 EFMS(:,j)=[]; endend
Substrate reaction number
Slide10Processing of flux modes in matlab®
plot(EFMS($$,:)*10/3,EFMS($$,:)*37.287/3,
's','MarkerFaceColor','k')
Product reaction number
Biomass reaction number
Carbon atoms product
Carbon atoms biomass
Carbon atoms substrate
Slide11Processing of flux modes in matlab®
indices=find(EFMS($$,:)==max(EFMS($$,:)));
MaxYield=EFMS(:,indices);
Product reaction number