KW-0409

[Antonialock]

pombe fxn1 is picking up a mapping to cellular iron ion homeostasis KW-0409

I think to the best of current knowledge this protein is involved in iron-sulfur cluster assembly, it doesn't regulate the process per se

[sylvainpoux]

@marcfeuermann

Hi Marc,

could you have a look to this. I suppose we should delete the KW from FRDA_SCHPO (O74831) but I see we are not up-to-date in term of pombase Xref and there is at leaset one paper for this protein (PMID:24997422)

Thanks

Sylvain

[Antonialock]

e.g. for yeast

"Regarding iron sensing, a combination of biochemical, biophysical and genetic data indicate that [2Fe–2S]-bridged Grx3/4 homodimers interact with the BolA-like protein apo-Fra2 and lead to the formation of a [2Fe–2S]Fra2-Grx3/4 complex in which Fra2 substitutes one Grx3/4 monomer and one glutathione molecule (Fig. 1) (Kumanovics et al. 2008; Li et al. 2009). In vitro data have demonstrated that this is a thermodynamically and kinetically favorable process (Li et al. 2011a). Further data have indicated that, under iron-sufficient conditions, the [2Fe–2S] cluster is transferred from the Fra2-Grx3/4 complex to Aft1/2 transcription factors. As a result, Aft1/2 factors form [2Fe–2S]-bridged homodimers with decreased affinity for DNA that dissociate from their target promoters and transcription of the iron regulon decreases"

https://link.springer.com/content/pdf/10.1007%2Fs11274-017-2215-8.pdf

[Antonialock]

"when iron becomes scarce, Aft1 accumulates in the nucleus, binding FeREs and activating transcription (Yama-guchi-Iwai et al. 2002)."

[marcfeuermann]

Hi, I'm currently updating pombe's frataxin. KW-0409's definition is "Protein involved in the storage of iron" and mapped to GO:0006879; cellular iron ion homeostasis. There is indeed not much literature about pombe's fxn, but just looking for S. cerevisiae I've found several papers stating that frataxin is indeed involved in iron storage (see few examples below). So this is why this KW has been applied to all the frataxins. So I would not remove the KW, until you convince me that pombe frataxin is not behaving like the other frataxins. I let you know when pombe entry will be updated and integrated. Thanks a lot. Marc.

From PMID:12149269 "Frataxin is required for maintenance of normal mitochondrial iron levels and respiration. The mature form of yeast frataxin (mYfh1p) assembles stepwise into a multimer of 840 kDa (apha-48) that accumulates iron in a water-soluble form... We have proposed that the apparent involvement of frataxin in so many diverse processes could be explained if the basic function of this protein were to provide an iron storage mechanism to keep iron in a bioavailable and nontoxic form (17). Indeed, titration of the mature form of yeast frataxin (mYfh1p) with Fe(II) under aerobic conditions results in stepwise assembly of a 48-subunit multimer with a molecular mass of 840 kDa and a hydrodynamic radius of 11 nm that sequesters 50 atoms of iron/subunit and forms iron-rich cores with a diameter of 2– 4 nm (23, 24)... In this study, we investigate the iron oxidation reaction of yeast frataxin. Our results support a direct role for frataxin in iron metabolism."

From PMID:18393441
Structural Basis of the Iron Storage Function of Frataxin from Single-Particle Reconstruction of the Iron-Loaded Oligomer

"Proteins from both the frataxin and ferritin superfamilies have been shown to assemble into large multimeric particles capable of detoxifying iron by catalyzing the oxidation of Fe(II) to Fe(III) and storing large amounts of the metal in the form of a ferrihydrite mineral within the core of the particles... frataxin and its bacterial homologue CyaY may exist in several oligomeric states in solution, with varying amounts of stored iron..."

and

"In contrast to ferritin in which the pore at the 4-fold axis is highly hydrophobic and probably has a minor role in metal trafficking, the negative surface potential at the outer side around the pore in frataxin may allow positively charged ions to enter the core of the particle, while the positive surface potential at the inner side would prevent these ions from escaping into the mitochondrial matrix."

From PMID:18327971 Intracellular iron transport and storage: from molecular mechanisms to health implications.

"The proposed function of frataxin is mitochondrial iron homeostasis, including iron storage and transport, heme synthesis, and ISC formation, as well as antioxidant defense. "

[Antonialock]

It looks like the ferritin-like/storage function of frataxin was later refuted? It seems like the current consensus is that frataxin detoxifies and chaperones iron

PMID:15472712 "Iron-induced oligomerization of yeast frataxin homologue Yfh1 is dispensable in vivo" "We identified a mutant Yfh1 defective in iron-induced oligomerization. This mutant protein was able to replace functionally wild-type Yfh1, even when expressed at low levels, when mitochondrial iron levels were high and in mutant strains having deletions of genes that had synthetic growth defects with a YFH1 deletion. The ability of an oligomerization-deficient Yfh1 to function in vivo suggests that oligomerization, and thus oligomerization-induced iron storage, is not a critical function of Yfh1. "

PMID:20307653 "Evidence that yeast frataxin is not an iron storage protein in vivo." "The assembly of Yfh1p in vitro is a stepwise process that requires the presence of Fe(II). Fe(II) is converted into Fe(III) during the oligomerization process, yielding ferritin-like particles of 24 or 48 subunits. Yfh1p monomers are arranged into trimers within these particles, which contain up to 2400 iron atoms. Frataxin has been compared to ferritin, despite major structural differences, since both proteins can convert redox-active iron into an inert mineral through ferroxidation activity. These findings led several authorsto suggest that frataxin not only promotes the biogenesis of iron-containing proteins (through monomeric or small oligomeric forms ofthe protein), but also detoxifies surplus iron in the mitochondria (through the formation of ferritin-like frataxin particles), thereby mediating a major antioxidant mechanism.

It remains unclear, however, whether the iron storage properties of frataxin demonstrated in vitro play a role in, or are required for, in vivo function. In a recent study, Gakh et al. showed that Yfh1p oligomerization in vivo is induced by iron, heat stress and overproduction of the monomer. However, they did not show iron storage in Yfh1p multimers in vivo. We also previously observed that overexpression of YFH1 resulted in an increased level of Yfh1poligomerization in vivo, but the shift in Yfh1p distribution after gel filtration was not accompanied by a shift in iron distribution, suggesting that iron was not stored in the multimers. In the present study, we investigate this issue further by analyzing the physico-chemical properties of iron accumulated in the mitochondria of different yeast strains in the presence of various amounts of Yfh1p. We conclude that Yfh1p did not store iron in vivo under our experimental conditions.

It looks like oligomerization is important for heme biosynthesis: PMID:27026703 "Each interaction site involves one ferrochelatase monomer and one frataxin trimer, with conserved polar and charged amino acids of the two proteins positioned at hydrogen-bonding distances from each other. One of the subunits of the Yfh1 trimer interacts extensively with one subunit of the ferrochelatase dimer, contributing to the stability of the complex, whereas another trimer subunit is positioned for Fe2+ delivery."

PMID:23344952 The molecular basis of iron-induced oligomerization of frataxin and the role of the ferroxidation reaction in oligomerization. For the ferroxidation-deficient D79A/D82A variant of Yfh1, iron-dependent oligomerization may still take place, although >50% of the protein is found in the monomeric state at the highest iron-to-protein ratio used. This demonstrates that the ferroxidation reaction controls frataxin assembly and presumably the iron chaperone function of frataxin and its interactions with target proteins.

[Antonialock]

so it has iron chaperone activity (and ferroxidase activity?) assisting in iron incorporation into metallo-sulfur cluster [2Fe-2S] assembly heme biosynthesis ?? (but it doesn't look like storage?)

[marcfeuermann]

I'm sorry, I did not understand your request. The KW was not wrong at the time entries were annotated and the papers used were quite convincing. I will have to update all the frataxins annotations (and read the corresponding literature, and not only about yeasts) which requires quite a lot more time than just correcting a KW. I will put this on my long TO DO list :-) Regards, Marc.

[Antonialock]

ok cheers

[pgaudet]

@Antonialock I think this is gone - can you check ?

[ValWood]

We would filter this locally so it would be difficult for us to know if the more global issue is fixed. If @marcfeuermann is happy the ticket can be closed.

[ValWood]

actually, the mapping wasn't filtered and it is still there: https://www.pombase.org/gene/SPCC1183.03c

[pgaudet]

The Keywords I see in the UniProt entry are Heme biosynthesis, Ion transport, Iron storage, Iron transport, Transport

but not iron homeostasis. Where do you see that ? (Heme biosynthesis seems odd too @ggeorghiou )

[ggeorghiou]

There is no keyword for iron homeostasis but the keyword that maps to cellular iron ion homeostasis is Iron Storage (KW-0409) which is mapped to GO: GO:0006879 - cellular iron ion homeostasis

[pgaudet]

My question was, why map transport KW to homeostasis ? Why not to transport ? That seems the safest mapping.

[ValWood]

transport isn't correct for frataxin, see above. Maybe remove the KW?

[suzialeksander]

iron storage no longer appears on the above linked pombase site.

[ValWood]

This seems to be about KW-0409 which is still present.