Re: [sbml-groups] Flux of branched amino acids in bacillus subtilis

[Lucian Smith]

On Thu, Apr 1, 2021 at 6:43 AM caroline Fukuda <carolin...@gmail.com> wrote:

Hi, 

I'm a beginner student at metabolic engineering, and I'm analysing the valine production of bacillus subtilis on optflux. But when I do the wild type simulation, the values of valine, leucine and isoleucine fluxes are null. I think that's because the reactions on SBML files are incomplete, but I don't know what to do about it. Can someone give me a guidance?

 Hi, Caroline!  Happy to answer your questions, though we might need some more information.  Also, you managed to find the 'sbml-groups' list, which technically is about the 'groups' package for SBML, not general SBML questions like yours.  That's better suited to 'sbml-discuss', which I've copied on this message, and should get you more responses.

So, I haven't used OptFlux before, but a cursory glance makes it look like it's a flux balance analysis (FBA) tool.  Models used in FBA have constraints on the reaction rates, but do not set the reaction rates themselves--the idea is to perform your analysis and discover particular possible values of reaction rates that would satisfy the given conditions.  These values are then the likely values of the system at steady state in whatever condition the FBA constraints were set to (often 'max growth').

I'm not sure if the 'simulation' you want to perform is a time-course simulation, but if so, the flux values you obtained from an FBA analysis would not be appropriate, since those values would apply at steady state only.  So if you do want a time course analysis, here are the options I can think of:

* Find another non-FBA type model of the system you're using.

* Find out what the reaction rates are from the literature.

* Put in 'default' reaction rates based on mass action (or similar).  You might be able to fill in the rate constants with values that make the model match an FBA analysis?  I haven't tried this myself, but if (for example) the FBA tells you that a given reaction rate is X, and that the concentrations of the reactants are S1 and S2, if you assume mass action kinetics, you know that X = k*S1*S2, and you can solve for k.

There are a variety of tools out there to help you manipulate the model; I know COPASI is popular, and our own lab produces the Tellurium suite of python packages that might also work for you.  Other people here might suggest their own tools.

Good luck, and let us know if you have any other questions!

-Lucian Smith

[Matthias König]

Hi Caroline,

in case you are running FBA (constraint-based) simulations:

1. Your medium could be too large; E.g. if you have a full medium with all amino acids valine, leucine and isoleucine can most likely by synthesized from other precursors so a flux through the exchange is not required.

You should reduce the medium (exchange reactions) and see if you get flux through the reactions.

2. Your subnetwork could be disconnected/dead ends. You will never get flux through it. This could be the case of missing reactions. You could force flux through the import and see if the model optimizes. I.e. use a minimal exchange set and set an uptake of valine or leucine or isoleucine. Use as an objective flux through the uptake. This will tell you if you can take up valine and the other amino acids. This should be the case because they go via a few reactions to the TCA cycle where there backbone can be completely oxidized.

3. Perform FVA (flux variability analysis) to see if flux through the reactions is possible.

4. Also visualization can be very helpful to see if things are connected or not.

5. Try to run parsimonious FBA (mimimzing the sum of fluxes in addition to your objective). With classical FBA often large futile cycles exist. The branched chain amino acids are synthesized in a large series of reactions and also incorporation into TCA takes a few reaction steps. There could just be cheaper solutions especially if these are not part of the biomass.

FBA is just a mathemetical optimization and most often does not give physiological results. If there is a cheaper solutions to fullfill the optimization objective (often biomass) then this will be used.

Also you should check if valine/isoleucine/leucine are part of your biomass function you optimize (if they are there should be an uptake because this is most often the cheapest solution).

Best Matthias

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Matthias König, PhD.
Junior Group Leader LiSyM - Systems Medicine of the Liver
Humboldt Universität zu Berlin, Institute of Biology, Institute for Theoretical Biology
  https://livermetabolism.com
koni...@googlemail.com

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Tel: +49 30 2093 98435