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Source ontology files for the Gene Ontology
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NTR ferric iron reductase (for non siderophore) #27593

Open ValWood opened 2 months ago

ValWood commented 2 months ago

I am trying to locate a ferric iron reductase term to curate frp1.

Currently it is annotated to ferric-chelate reductase (NADPH) activity (GO:0052851) Catalysis of the reaction: 2 Fe3+-siderophore + NADP+ + H+ -> 2 Fe2+-siderophore + NADPH.

and although it may have this activity if it also operates in the siderophore system, its known role is in the is in

reductive iron assimilation (GO:0033215) A process in which iron is solubilized by reduction from Fe3+ to Fe2+ via a cell surface reductase and subsequent transport of the iron across the membrane by iron uptake proteins.

via fio1/fip1 transporter system (Ftr1/Fet3 equivalent)

and this iron is not chelated

"However, not all ferric iron reductases exclusively target chelated iron. Some ferric iron reductases can act on unchelated ferric iron as well. For example, membrane-bound ferric reductases in bacteria and yeast, such as the Feo system and the Ftr1/Fet3 complex, are capable of reducing both chelated and unchelated ferric iron."

So which term would I use for a ferric iron reductase (non-chelated iron)

cc @Antonialock you may know

ValWood commented 2 months ago

Expert says

"With respect to high affinity Fe uptake via Fio1/Frp1 machinery, it is known (based on S cerevisiae data) that Frp1 plays a crucial role for reducing Fe3+ to Fe2+ prior its passage across the membrane through Fio1/Frp1 heterocomplex. We know that Frp1 has a huge ferrireductase activity at the cell surface. Based on the Orfeome, Frp1 localizes at the cell surface."

and "Concerning your questions, as far as know, there are no papers reporting any functional roles for Frp1 and Frp2 with respect to siderophore (ferrichrome) uptake in S pombe."

So it seems PomBase and SGD @edwong57 are using the wrong term here, and I cannot find the correct term. I will transfer this to the ontology tracker for the new term.

ValWood commented 2 months ago

New term requested is

ferrireductase activity We know it exists, but I cannot locate it in Rhea entry and I don't know what the reaction would be?

pgaudet commented 2 months ago

RHEA:71767 ? https://www.ebi.ac.uk/QuickGO/term/GO:0004322 ? (since the reaction is not directional)

ValWood commented 2 months ago

Hmm, that looks correct , but the other direction (oxidation after import) in this pathway is performed by https://www.pombase.org/gene/SPAC1F7.08 (fio1) Is it definitely not directional?

ValWood commented 2 months ago

It would seem weird to annotate the reductase and the oxidase to the same term though wouldn't it? They are represented by different gene products, so presumably directional activity terms should exist?

The reductive HA pathway involves three sequential steps: (i) the initial reduction of ferric (Fe3+) to ferrous (Fe2+) iron by a dedicated membrane-bound ferric reductase encoded by FRE1 and FRE2 genes; (ii) the re-oxidation to ferric iron (Fe3+) by the multicopper ferroxidase (ferroxidase) encoded by the FET3 gene; ... https://www.mdpi.com/2073-4425/11/11/1296