canonical glycolysis ancestry

[ValWood]

canonical glycolysis is a descendant of "GO:0046939 nucleotide phosphorylation" which seems odd?

some nucleotide phosphorylaton events are part_of glycolysis?

[deustp01]

Yes. ADP is phosphorylated to form ATP in the course of glycolysis, as shown in the screenshot from the canonical glycolysis quickGO page:

@ukemi I think we decided there was no alternative to this, because ATP generation is a central feature of glycolysis?

[ValWood]

I would expect to see ancestry aligned with the process, but "nucleotide phosphorylation" is more like a MF that is part of the process?

[ValWood]

Actually, It looks really strage to have a reaction (ATP generation from ADP) as a parent of the entire pathway. @ukemi Does that model in Noctua OK?

[pgaudet]

ATP generation from ADP was obsoleted in Jan 2023, and I have now made 'glycolytic process' is_a 'generation of precursor metabolites and energy'.

Thanks, Pascale

[ValWood]

Should gluconeogenesis also have the parent 'generation of precursor metabolites and energy'.?

[pgaudet]

This is a question for @ukemi and @deustp01 , but based on the definition of gluconeogenesis, "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol. " - I dont think so?

Also, from the change log in QuickGO, it looks like gluconeogenesis was never is_a 'generation of precursor metabolites and energy'.

[pgaudet]

The def of 'generation of precursor metabolites' is "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances."

@ukemi @deustp01 can we have a list (even partial) of these precursor metabolites?

[deustp01]

@ukemi can we have a list (even partial) of these precursor metabolites?

The list, even a partial one, will be complicated, full of taxon constraints, and, unless also provided with tissue- and physiological-state- constraints, will be wildly misleading. For example, in green plants carbon dioxide, via photosynthesis, looks like a precursor. In healthy humans long chain fatty acids are precursors but mostly in the fasting state and never in red blood cells. And so on.

I think we need two preliminary discussions here. First, what are the use cases for such lists? If we find good ones, then a second one is needed to find a strategy that real curators can apply to construct minimal lists that are accurate, maintainable, and responsive to the use cases.

And perhaps we also need to think of alternative approaches. For example, given a good set of GO-CAMs (not out of reach for eukaryotic energy metabolism), and really robust tools to identify "provides input for" relationships between activities both within a single GO-CAM / process / pathway and between them, the precursors fall out of the pathway annotations (including real ones not expected per the textbooks).

[ValWood]

GO:0006091 generation of precursor metabolites and energy has always been a bit of a problem term. Its a bit of a fudge to groups terms related to energy generation for enrichment and slimming (many of which would not slim elsewhere). These include glycolysis, TCA cycle, respiratory chain, photosynthesis. The current children are below:

I have always been a bit confused by the "generation of precursor metabolites"
part of the term label (although the def does seem to restrict to "energy generation")

The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

Although the term is clunky, it does seem to work as an "annotation bin" to collect together energy generating processes.

GO:0015980    energy derivation by oxidation of organic compounds	is_a
GO:0009765    photosynthesis, light harvesting	is_a
GO:0006069    ethanol oxidation	is_a
GO:0006740    NADPH regeneration	is_a
GO:0019684    photosynthesis, light reaction	is_a
GO:0061719    glucose catabolic process to pyruvate utilizing ADP	is_a
GO:0015975    energy derivation by oxidation of reduced inorganic compounds	is_a
GO:0009052    pentose-phosphate shunt, non-oxidative branch	is_a
GO:1902224    ketone body metabolic process	is_a
GO:0022900    electron transport chain	is_a
GO:0043467    regulation of generation of precursor metabolites and energy	regulates

GO:0061722    sulphoglycolysis

GO:0015980 energy derivation by oxidation of organic compounds is_a GO:0009765 photosynthesis, light harvesting is_a GO:0006069 ethanol oxidation is_a GO:0006740 NADPH regeneration is_a GO:0019684 photosynthesis, light reaction is_a GO:0061719 glucose catabolic process to pyruvate utilizing ADP is_a GO:0015975 energy derivation by oxidation of reduced inorganic compounds is_a GO:0009052 pentose-phosphate shunt, non-oxidative branch is_a GO:1902224 ketone body metabolic process is_a GO:0022900 electron transport chain is_a GO:0043467 regulation of generation of precursor metabolites and energy regulates GO:0061722 sulphoglycolysis