reference for irreversible malate dehydrogenase during anaerobic simulation

[mperisin-lallemand]

Description of the issue:

The anaerobicModel.m script indicates that malate dehydrogenase (r_0173, r_0714) should be constrained to zero flux:

%Block oxaloacetate-malate shuttle (not present in anaerobic conditions) model.lb(strcmp(model.rxns,'r_0713')) = 0; %Mithocondria model.lb(strcmp(model.rxns,'r_0714')) = 0; %Cytoplasm

Is there a reference for this observation?

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Done this analysis in the main branch of the repository
• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue

[edkerk]

The anaerobicModel.m script indicates that malate dehydrogenase (r_0173, r_0714) should be constrained to zero flux:

Note that the lower bound is constrained to zero flux, the reactions can still carry a flux of 0 or higher. This seems to have been introduced when yeast7 was expanded to an enzyme-constrained model. It seemed necessary for that model to replicate the observed phenotype. See in the Appendix:

It is not an ideal situation, to change such reaction bounds specifically for one condition. We should consider whether these reactions should be reversible, and if, they should also be reversible in anaerobic conditions.

[jiuia]

@edkerk Hi! I have two questions about yeast8GEM working in anaerobic conditions: 1, what can I do to remove s_3714 from the reaction (r_4041)? and 2, how do I change the biomass pseudoreaction reaction equation? Looking forward to your reply!

[edkerk]

The function code/otherChanges/anaerobicModel can generate this "anaerobic model". If you only interested to remove s_3714 from r_4598 (the biomass reactions have been reconfigured, such that cofactors like heme are in their own pseudoreaction), you can modify the respective lines.

[jiuia]

@edkerk Thank you very much for your reply! May I ask which solver was used (cobra，raven or others)? Because I keep getting errors when I run it in cobra's environment!

[jiuia]

@edkerk like that "Reference to a non-existent field 'rxns'.
Error setParam (line 49):index=find(strcmp(rxnList{i},model.rxns),1);"

[edkerk]

@jiuia I suggest you open a Discussion thread where you explain exactly what commands you ran and what error message you observed. Then this Issue can focus on malate dehydrogenase reversibility. Your error message from setParam suggest that the model is not correctly loaded.

[jiuia]

@edkerk ok fine!

[edkerk]

Work on an updated anaerobic model are discussed in #352