1. Veronique Beckers veronique.beckers@uni-saarland.de
Exercise Systems & Synthetic Biotechnology elementary flux mode analysis
Veronique Beckers

2. 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?
Processing of flux modes in matlab®

3. Update network construction
Project:
5 groups
Corynebacterium glutamicum
Aspergillus niger
Saccharomyces cerevisiae
Escherichia coli
Pseudomonas putida
Network construction:
Which pathways?
Information required: stoichiometry, reversibility, localization, biomass synthesis requirements
Biomass synthesis: protein composition and precursor demand
substrates:
Glucose
Xylose
Saccharose
Fructose
Glycerin
Lactate

4. What are elementary flux modes?
Mode = a single independent pathway
Number of modes = the number of all
possible, independent flux distributions
in a steady state

5. What 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

6. What knowledge can we gain from elementary mode analysis?

7. Processing of flux modes in matlab®
rformulas={' --> A'
'A --> C'
'C --> P + D'
'P --> '
'A --> B'
'B <==> C'
'B --> P'
' <==> B'
'D --> '};
mnet=CalculateFluxModes(rformulas);

8. Matlab principles

9. What 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)=[];
Substrate reaction number

10. Processing of flux modes in matlab®
Carbon atoms substrate
plot(EFMS($$,:)*10/3,EFMS($$,:)*37.287/3,'s','MarkerFaceColor','k')
Biomass reaction number
Carbon atoms biomass
Product reaction number
Carbon atoms product

11. Processing of flux modes in matlab®
Product reaction number
indices=find(EFMS($$,:)==max(EFMS($$,:)));
MaxYield=EFMS(:,indices);