I am about to reconstruct a metabolic network for a chemelithiautotroph thiobacillus. It uses Co2 as the carbon source and Thiosulfate as the energy source. I have setted a central metabolsim for this micro organism inculding Calvin cycle (The dark part), TCA cycle, Glycolysis and other common pathway but when in comes to sulfur metabolsim in which Thiosulfate is consumed and terationathe is produced then terathionate oxidizes and so on. When I add sulfur metabolsim network become infeasible and there is no link between central metabolsim and sulfur. I'd be very thankful if anyone could help me.
Hi Meiya
My problem is finiding a proper reaction for linking sulfur and central metabolism.What happens inside the cell is that the reduction of Co2 is coupled to oxidation of sulfur compound But there is no reaction associating these two,Co2 reduction produces Glyceraldehyde 3 phosphate which enters glycolysis and sulfur compound oxidizes (in this case Thiosulfate) to tetrathionate and later to sulfate(as the main product) and sulfur .As you mentioned when I try to limit the uptake rate of thiosulfate the infesibility appears.I use FBA method,Do you have any idea to link these to parts?A redox reaction or somthing like that.
Best Regards
Sepideh
Hi Sepideh,
I did a quick search in KEGG using as reference one Thiobacillus so I guess you will have to taylor it to your microorganism in concrete but, you could link thiosulphate with
a) thiosulphate->sulfide->homocysteine (and in this last step succinate is produce in a paralel reaction, have a look to the map: http://www.genome.jp/kegg-bin/show_pathway?org_name=tbd&mapno=00920&mapscale=&show_description=hide)
b) to the cysteine and methionine metabolism:
sulfide->->cysteine-->mercaptopyruvate-->pyruvate
(see map: http://www.genome.jp/kegg-bin/show_pathway?org_name=tbd&mapno=00270&mapscale=&show_description=hide)
I hope it helps or at least it gives you some ideas.
Also I would like to ask you which software are you using for the FBA?
Thanks and good luck,
Eva
Should not the link be provided by the ATP requirement for growth (and maintenance)? Linking thiosulfate oxidation to growth would then require an estimate of the overall P/O for thiosulfate oxidation - and the total ATP requirement for biomass formation and maintenance.
Hi Eva
Thanks a lot for answering my question.I took a look at those links,My organism is a little bit different from Thiobacillus dentirificants.It uses thiosulafte and through S4 pathway produces sulfate and sulfur.My network is not big at the moment and it does not contain Amino acid metabolism.I use Matlab for FBA.I tried to link thiosulfate oxidation to central metabolism by using a reaction which produces ATP but the network is still infeasible
Hello Jack
Thanks a lot for answering my question,I used the following reaction to create a link between sulfur metabolism and central metabolism but it did not work
Na2S2O3+2O2+H2O+4ADP+4Pi=>Na2So4+H2SO4+4ATP
the p/o ration for this organism is 1.12.
Due to the infeasibility I can not expand the network now it just includes central metabolism and 4 reaction of sulfur metabolism one for thiosulfate exchange,2 for thiosulfate oxidation and one for tetrathionate conversion to sulfate and sulfur
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