Missing parent: GO:0006798 polyphosphate catabolic process (plus other issues)

[ValWood]

• GO term ID and label for which you request a new superclass

  GO:0006798 polyphosphate catabolic process

• New superclass (parent) suggested

generation of precursor metabolites and energy (GO:0006091)

• Reference(s), if appropriate

Since polyphosphate is an energy storage molecule, should generation of precursor metabolites and energy (GO:0006091) be a parent?

[deustp01]

Since polyphosphate is an energy storage molecule

But Wikipedia classifies ATP, ADP and other NTPs as polyphosphates: "In biology, the polyphosphate esters ADP and ATP are involved in energy storage." First quibble: two phosphates seems a bit scant for "poly". More important quibble: most polyphosphate is simply that, an inorganic polymer of phosphate units. Is this common form involved in energy storage?

[ValWood]

i) I'd also assumed poly was >2

ii) My understanding is that excess phosphate is stored as polyphosphate in the vacuole https://www.pombase.org/reference/PMID:34147496

Maybe this is sequestering rather than storage?

[deustp01]

Arthur Kornberg worked on polyphosphate at the end of his career. Look there for wisdom? Rao NN, Gómez-García MR, Kornberg A. Inorganic polyphosphate: essential for growth and survival. Annu Rev Biochem. 2009;78:605-47. doi: 10.1146/annurev.biochem.77.083007.093039. PMID: 19344251.

[ValWood]

I'll take a look at this.

[pgaudet]

According to wikipedia there are roles other than energy storage: https://en.wikipedia.org/wiki/Polyphosphate:

• formation of channels across the living cell membranes
• blood coagulation

Would we not be creating a true path violation by adding this new parent?

[ValWood]

yep, will close

[ValWood]

Just to note, the reason this came up is because it doesn't slim with the generic slim (or the Pombase slim) .

Although should I add:

GO:0006796 phosphate-containing compound metabolic process The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.

as a parent of

GO:0006797 polyphosphate metabolic process Biological Process The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.

I would then add GO:0006796 phosphate-containing compound metabolic process to the PomBase slim. This would help with a lot of the "drop out".

https://www.pombase.org/gene_subset/non_slim_with_biological_process_annotation

[pgaudet]

Maybe this terms is too generic? ie as it is, it's described as a polyphosphatase activity. The BP annotations could be moved to more process-like terms such as phosphate storage (would need a new term) and blood coagulation.

All annotations are to yeasts and bacteria, so phosphate storage or homeostasis could be better annotations. What do you think ?

[ValWood]

but the phosphatase is mobilizing the storage from the vacuole. Homeostasis isn't worng, but it doesn't fully describe the breakdown of the storage molecule. Are you proposing that polyphosphate catabolic process is obsoleted?

[pgaudet]

Are you proposing that polyphosphate catabolic process is obsoleted?

yes, and that we create a better BP. Or we can 'reuse' the term since it has only been used to describe phosphate storage (or utilization?)

[ValWood]

@pgaudet do you have any objection if I added "phosphate utilization" ? this would resolve a lot of my issues and we have sulfur, carbon, nitrogen utilization.

This would enable me to capture the pathway and its regulation, none of the other terms work. I have tried homeostasis, but it isn't quite right and I can't capture the upstream positive and negative ve regulation of the starvation response using this term... I want capture the signalling to switch on (and off) the genes which are involved in the metabolism, transport and release from storage etc of extracellular phosphate in response to phosphate starvation (or replete).

We can probably then obsolete some of the terms describing single steps like"polyphosphate catabolic process"