Merge 'ferric iron transmembrane transport' into 'ferric iron import across plasma membrane'

[pgaudet]

This ticket #14892 will lead to a lot of changes, so I am trying to split up some sub-issues.

Merge 'GO:0015683 ferric iron transmembrane transport' into 'GO:0098706 ferric iron import across plasma membrane'

• add taxon restriction 'only in bacteria'.

• Only bacteria can transport ferric iron (3+) across membranes(PMID:24312900); in mammalian cells (and in fungus) ferric iron is internalized by endocytosis, and reduced to ferrous iron (2+) for intracellular (ie mitochondrial) transport.

Tagging @ValWood @RLovering for input since you have commented on the other ticket; but comments by everyone is welcome.

Thanks, Pascale

[ValWood]

This makes sense to me.... PomBase have no annotations to either term...

[pgaudet]

Also need to change the reference: PMID:8321236 talks about reductive iron transport

[pgaudet]

Added comment "In most organisms, ferric iron (3+) is reduced to ferrous iron (2+) before being transported into the cell. Some infectuous bacteria can extract the ferric iron bound to the the host's transferrin and transport it via a transmembrane transporter (for example, TbpAB of N. meningitidis and N. gonorrheae)."

[pgaudet]

@marcfeuermann Can we review this together ?

[RLovering]

Based on the figure I added to the previous ticket I agree that transmembrane transport of Fe+ does not occur in mammals. However, Fe3+ does get into the cells by endocytosis, but does not cross the membrane until it is reduced to Fe2+. Hopefully a BP term will be available for the proteins that are responsible for the endocytosis of Fe3+ Thanks Ruth

[pgaudet]

@RLovering yes, of course.

[pgaudet]

Hi @amandamackie

Based on the papers you provided in https://github.com/geneontology/go-annotation/issues/2054#issuecomment-413070749

I now wonder if there is such as thing a transmembrane transport or ferric iron; do you know ? It looks like ferric iron is only transported in complex with sideriphores, is this right ?

@jimhu-tamu @dsiegele Comments ?

If there are no instances of ferric acid TM transport I will obsolete the terms.

Thanks, Pascale

[dsiegele]

Hi Pascale,

There are examples of ferrous (Fe2+) and ferric (Fe3+) iron uptake systems among prokaryotes that are used to transport Fe2+ and Fe3+ across the plasma membrane without being bound to a siderophore or as part of compound, such as ferric citrate . I haven't looked at the definitions of 'GO:0015683 ferric iron transmembrane transport' and 'GO:0098706 ferric iron import across plasma membrane' to figure out which one is appropriate.

uptake of Fe3+ across the plasma membrane in bacteria: Miethke M. Molecular strategies of microbial iron assimilation: from high-affinity complexes to cofactor assembly systems. Metallomics. 2013 Jan;5(1):15-28. PMID: 23192658 doi: 10.1039/c2mt20193c.

• This system has an outer membrane protein that is able to take iron away from ferritin or lactoferrin and transport it to a Fe3+ binding protein in the periplasm. The periplasmic protein then delivers the Fe3+ to a transport system located in the cytoplasmic membrane.

uptake of Fe2+ across the plasma membrane in bacteria: Cheryl K. Y. Lau Karla D. Krewulak Hans J. Vogel Bacterial ferrous iron transport: the Feo system FEMS Microbiology Reviews, Volume 40, Issue 2, 1 March 2016, Pages 273–298, https://doi.org/10.1093/femsre/fuv049

predicted uptake of Fe2+ across the plasma membrane in Archaea: Leyn SA, Rodionov DA. Comparative genomics of DtxR family regulons for metal homeostasis in Archaea. J Bacteriol. 2015 Feb;197(3):451-8. doi: 10.1128/JB.02386-14. PMID: 25404694

• This is predicted based on sequence similarity to the bacterial Feo system. I haven't looked for articles with experimental evidence.

I haven't found any articles about Fe3+ uptake across the plasma membrane in Archaea, but I can look further if you want.

[pgaudet]

Thanks @dsiegele this is very useful.

The 'transmembrane transport' term would also allow to annotate Fe3+ export (ie to an 'export' child that is no in the ontology), but I don't think this exists; do you know?

Thanks, Pascale

[pgaudet]

• Merged terms
• Changed label: ferric iron import across cell outer membrane
• Changed definition: The directed movement of ferric iron (Fe(III) or Fe3+) ions from outside of a cell, across the cell outer membrane and into the periplasmic space."
• Added comment: Ferric iron is rarely transported in the free form. Some bacteria have a system in which an outer membrane protein takes iron away from host ferritin or lactoferrin and transport it to a Fe3+ binding protein in the periplasm. The periplasmic protein then delivers the Fe3+ to a transport system located in the cytoplasmic membrane. Consider also GO:0015891 siderophore transport.
• Added taxon constraint: only_in_taxon some Bacteria

I will leave the ticket open until the rest of the changes in this branch are done, so I can update the comment to include the other mechanisms of transport.

[pgaudet]

Moved comment to MF 'GO:0015091 ferric iron transmembrane transporter activity'