Yeast Frequently Asked Questions
Q: What's the difference between the two yeast reconstructions?
A: There are three primary differences* between iFF708 and iND750:
The relationships between the ORFs, transcripts, proteins, and reactions are now directly accounted for in iND750 as Boolean logic statements. You can download the gene-protein-reaction associations here.
iND750 accounts for eight cellular localizations (extracellular space, cytosol, mitochondrion, peroxisome, nucleus, Golgi apparatus, vacuole, and endoplasmic reticulum) whereas iFF708 only accounts for three (extracellular space, cytosol, and mitochondrion).
iND750's reactions are both elementally and charge-balanced (no net gain of mass or charge). The formula and charge of the metabolites were determined based on their ionization state at pH 7.2.
Additional minor changes include: revised gene functions based on recent literature reports; updated gene names and Enzyme Commission (EC) numbers; removal of redundant compound abbreviations, duplicated reactions, and generic metabolites (e.g., "ceramide" has been replaced with 2 specific moeities).
Q: What's the difference between a transport reaction and an exchange reaction?
A: The difference lies in the boundary. Transport reactions describe metabolite transport between cellular compartments. Exchange reactions describe metabolite transport across the system boundary.
Q: How do I optimize for biomass?
A: One way is to include a reaction in the stoichiometric matrix that consumes the biomass constituents from the network in the appropriate ratios and then optimize for this flux.
Q: Why am I not getting any growth in my simulation?
A: There could be several reasons for this. First, check that exchange fluxes are implemented correctly. For minimal medium simulations, allow the fluxes of NH4, SO4, Pi, H2O, K, Na, and CO2 to be unconstrained. Anaerobic simulations also require ergosterol, zymosterol, palmitoleate (C16:1), stearate (C18:20), oleate (C18:1), and linoleate (C18:2) to be freely exchanged. Next, check whether or not you can make the basic precursors from glucose. Create a demand reaction for each precursor and optimize for this flux. Finally, check that you can make each of the biomass constituents. Once you identify which ones you cannot make, you need to go through the metabolic routes and determine why.
Q: Are there any values available that I can compare my model's results with?
A: The following table has some simulation results for glucose minimal media simulations. All flux values are listed in mmol/g/hr.
|Glucose uptake rate||Glucose uptake rate||Intrasystem flux constraints||Unconstrained exchange fluxes||Growth rate|
ACOAH = 0
|O2, NH4, SO4, Pi, H2O, K, Na, CO2||.47793|
ACOAH = 0
|NH4, SO4, Pi, H2O, K, Na, CO2, ergosterol, zymosterol, palmitoleate (C16:1), stearate (C18:20), oleate (C18:1), linoleate (C18:2)||0.08534|