Gluconeogenesis (R-HSA-70263)

[ukemi]

• [x] Is the direction of R-HSA-372449 physiologically correct. Most of the references I am looking at say it exports citrate from the mitochondrion. I made this pathway, but the evidence for this transport being accomplished by this gene product is slim, some old experiments with isolated rabbit mitochondria as near as I can tell. So I left the gene product and the evidence off of the mouse pathway. I could add as a TAS because lots of reviews have un-referenced statements saying this is true???? Leads to complicated question about role of this reaction in gluconeogenesis (see comment)
• [x] Should we tidy up the arrows in the Reactome pathway diagram for R-HSA-372448? Looks hard (see comment)
• [x] Check Reactome subpathways for correctness (i.e., generalize task 1).
• [x] Check Reactome reactions and small molecules for conformity to RHEA.

[deustp01]

• Is the direction of R-HSA-372449 physiologically correct. Most of the references I am looking at say it exports citrate from the mitochondrion.

I need to review the gluconeogenesis pathway. The role of this reaction is to export mitochondrial PEP. On the one hand, this reaction as part of a variant source of carbon skeletons for gluconeogenesis was reviewed and accepted by R.A. Harris who is (was?) an authority. On the other, the standard pathway has oxaloacetate as the entity exported from the mitochondrial matrix to the cytosol, which is then converted to PEP in the cytosol. So is PEP export a bogus alternative source of carbons for gluconeogenesis? In that case the direction of citrate transport is irrelevant because there's no role for it here. Or not? Here is a paragraph from Wikipedia

In all species, the formation of oxaloacetate from pyruvate and TCA cycle intermediates is restricted to the mitochondrion, and the enzymes that convert Phosphoenolpyruvic acid (PEP) to glucose-6-phosphate are found in the cytosol.[27] The location of the enzyme that links these two parts of gluconeogenesis by converting oxaloacetate to PEP – PEP carboxykinase (PEPCK) – is variable by species: it can be found entirely within the mitochondria, entirely within the cytosol, or dispersed evenly between the two, as it is in humans.[27] Transport of PEP across the mitochondrial membrane is accomplished by dedicated transport proteins; however no such proteins exist for oxaloacetate.[27] Therefore, in species that lack intra-mitochondrial PEPCK, oxaloacetate must be converted into malate or aspartate, exported from the mitochondrion, and converted back into oxaloacetate in order to allow gluconeogenesis to continue.[27]

The "variable by species" bit may be critical here - it may be part of the differences in pathway organization among birds, rodents, and primates to support different needs for glucose. That in turn suggests that, at least for some species / some physiological states we may need to figure out how PEP gets exported from the mitochondrial matrix. More weeds!

[deustp01]

• Should we tidy up the arrows in the Reactome pathway diagram for R-HSA-372448?

Played some with the diagram and couldn't find a way to reduce the number of crossing reaction edges.

[ukemi]

Let's talk about the PEP transport on a weeds call. Isn't citrate transport a requirement as the function is an antiporter? Early experiments show that you can get PEP out of isolated mitochondria by adding citrate to the media.

[deustp01]

Let's talk about the PEP transport on a weeds call. Isn't citrate transport a requirement as the function is an antiporter? Early experiments show that you can get PEP out of isolated mitochondria by adding citrate to the media.

That could well be true, and then the Reactome reaction is backwards and we need some other mechanism for PEP export from mitochondria to cytosol, unless we can evade the need for PEP export. That's the weeds agenda item.

[deustp01]

Revisions of Reactome "Gluconeogenesis" to correct errors, align with Rhea, and (partly) sort out fate of mitochondrial PEP are finished. Note are here (David_and_Peter_notes > Gluconeogenesis 2022 > gluconeogenesis_notes and the pathway details exported from the Reactome web site as a document are in the same folder as gluconeogenesis_DB_ID_70263. @ukemi could you review the pathway document and, as time permits, use it to create mouse reactions?

Once the revisions are reviewed / approved, we can close the ticket.

[ukemi]

I'll go through these one by one and compare them to the mouse models I made. I know we talked about it, but I can't remember what we decide I should do about hypothetical reactions like "SLC25A1 may exchange mitochondrial PEP for cytosolic anion ". I think we decided I would go ahead and model this one. Apologies for my forgetfulness.

[deustp01]

I'd say, model it for now. Despite the lack of evidence the reaction appears to be quite popular among experts.

[ukemi]

Notes: NB. I don't have ll the reactants in the mouse models yet.

• [x] I'm not seeing the Rhea xrefs on the curators site (eg R-HSA-71783 -> RHEA:21434)). Am I supposed to? NO. Currently, Reactome reactions are mapped to Rhea ones using Rhea's mapping file, at release time, so they never get into our central database. An issue for future discussion is how to maintain links and track changes - should we hard-wire the correct links into the Reactome annotation?
• [x] Reaction Reaction:R-HSA-71783 is called "MDH1 reduces OAA to MAL" but it's catalyzed by MDH2. In mouse model: Gluconeogenesis 1. OOPS. MDH2 (mitochondrial) is correct - reaction name corrected.
• [x] SLC25A10 reaction leads us to mouse Gluconeogenesis 1. NOTED (also R-HSA-70613 comment and possibly the Got2, Pck1, and Pck2 comments further below). For the future do we want to consider identifying subtypes of gluconeogenesis as we did for glycolysis, perhaps as part of thinking about specific-specific differences in the role of gluconeogenesis that drive these alternative routes, e.g., how much gluconeogenesis proceeds from amino-acid-derived carbon skeletons versus lactate? Too big digression a into comparative biology?
• [x] R-HSA-198505 In the diagram oxaloacetate is called OA, but in the description is is referred to as OAA. There is also inconsistency in the overall pathway wrt OA or OAA (see R-HSA-198505 vs the output of R-HSA-70501. OOPS - "OA" is the Reactome abbreviation, even though OAA is also widely used. I will fix these instances and any others I find.
• [x] R-HSA-70613 represents the branch in mouse Gluconeogenesis 3.
• [x] Mouse Slc25a11 was injected into gluconeogenesis 3 between Got2 and Got1. But I can't find any real evidence that GOT2 is involved in gluconeogenesis other than the MF.
• [x] Mouse Slc25a13 was done but not Slc25a12. I added Slc25a12 to gluconeogenesis 3. Evidence for the function is IMP, but I can't find evidence that this paralog is used for gluconeogenesis. Should I leave the function and an evidenceless process? NOTED - Reactome practice would be to leave it. If one member of a protein family clearly enables something, and other members seem to share the features needed for that functiuon and haven't been shown to enable something else, they get annotated as candidate enablers.Historically we haven't taken tissue-specific expression into account (so localization to liver or kidney would be evidence in support of a role in gluconeogenesis while localization to skin would be evidence against) probably because of a combination of our tissue-agnostic annotation practice and the lack of good, consistent, systematic surveys of tissue-specific expression patterns for gene products. Another issue for future discussion - do we want to start to change this, with gluconeogenesis as an excellent use case?
• [x] For mouse, GOT1 to Pck1 is gluconeogenesis 3. Mdh1 to Pck1 is gluconeogenesis 1.
• [x] For mouse, the Pck2 branch is gluconeogenesis 2. There is no enabler for the mitochondrial transporter yet.
• [x] There is a typo in the blurb for R-HSA-198440. Stdies of rat. OOPS - fixed

[deustp01]

@ukemi OK to close? We'll surely come back to aspects of this as part of insulin signaling / integration of energy metabolism, but all the chore specific to gluconeogenesis look finished.