search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
220 stars 40 forks source link

siderophore transmembrane transporter activity, revise primary name #23199

Closed ValWood closed 2 years ago

ValWood commented 2 years ago

siderophore transmembrane transporter activity (GO:0015343) Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in).

could this term be renamed to siderophore-iron transmembrane transporter activity (would make more sense as the purpose is to transport iron)

Also it would match

GO:0033214 | siderophore-dependent iron import into cell

raymond91125 commented 2 years ago

  1. Siderophores (Greek: "iron carrier"), thus the purpose is fairly clear. "iron" is not included in the names of the parent term or any of the children terms. e.g. GO:0044718 siderophore transmembrane transport GO:0015344 siderophore uptake transmembrane transporter activity

  2. siderophore-iron transmembrane transporter activity is a "related" synonym for GO:0015343.

  3. However, from the label and definition, this term is not restricted to import into cell (at least it's not clearly stated).

raymond91125 commented 2 years ago

refs - https://en.wikipedia.org/wiki/Siderophore, PMID:20376388, PMID:31748738, PMID:17804665

ValWood commented 2 years ago

Siderophores (Greek: "iron carrier"), thus the purpose is fairly clear.

This is true, but it is really the Siiderophore-Fe complex that is transported. The siderophore (a small peptide synthesised and exported by fungi and bacteria) alone is only a carrier. It seems more precise to say siderophore-iron in the term name, anyone who does not know what a siderophore is, it will be more plainly obvious that iron is the transported compound of interest. The main focus in the term name should really be on the iron, not on the siderophore.

However, from the label and definition, this term is not restricted to import into cell (at least it's not clearly stated).

Perhaps import into cell should be clearly stated. Siderophores are only used for import across the plasma membrane.

In fact a function -process link could be instantiated between GO:0015343 siderophore transmembrane transporter activity and GO:0033214 | siderophore-dependent iron import into cell

raymond91125 commented 2 years ago

At least one gene annotated with siderophore transmembrane transporter activity, irtA in Mycobacterium tuberculosis, is demonstrated to be a siderophore exporter, by selective binding to non-ferrated siderophores [PMID:18461140]. Thus, if we are to distinguish importers from exporters, we need to:

  1. Review all annotations of siderophore transport terms, those that are not explicit about the direction.
  2. Make new directional child terms and reannotate.
pgaudet commented 2 years ago

Right - I think I saw that before; is this worth it ?

ValWood commented 2 years ago

wearing my haemochromotosis hat, I'm not bothered about the function process (I can do that at annotation time) , my reason for requesting this is that currently siderophore transporter is not a descendant of iron ion transporter :

Screenshot 2022-04-22 at 09 18 56

  1. so if a user retrieves all "iron ion transporters", "siderophore transporter" is excluded and Fe3+ is an iron ion (this is what lead me to the problem, I did a query and these known iron transporters were missing)

  2. "Siderophore transmembrane transport" is already under "iron ion transmembrane transport"

  3. The definition of GO:0015343 siderophore transmembrane transporter activity is Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in).

and the exact definition is "iron-siderophore transporter activity" so its correct use is as a "iron-siderophore transporter activity" -- if it has been otherwise used it has been used incorrectly. Replacing the name to match the narrower meaning, and adding the missing parent would. be ontology best practice (if anyone wants to annotate the transport of an actual siderophore without iron, they can request the correct term for this, as it will be much clearer that the existing term is not the right one)

  1. There is the additional issue that I had not noticed- siderophore-dependent iron import is not related to siderophore transmembrane transport at all in the graph. I think that likely these 2 terms could be merged and inherit the properties of both (import, transmembrane, iron, plasma membrane) Unless, there are siderophores that import iron via endocytosis...
ValWood commented 2 years ago

edited to replace the figure.

raymond91125 commented 2 years ago

4. There is the additional issue that I had not noticed- siderophore-dependent iron import is not related to siderophore transmembrane transport at all in the graph. I think that likely these 2 terms could be merged and inherit the properties of both (import, transmembrane, iron, plasma membrane) Unless, there are siderophores that import iron via endocytosis...

It seems to me that siderophore transmembrane transport concerns both directions thus not equivalent to siderophore-dependent iron import.

ValWood commented 2 years ago

Do you have an example? I thought siderophores were only involved in iron accumulation.

raymond91125 commented 2 years ago

PMID:18461140 -- "IrtA is involved in the export of non-ferrated siderophores" image

raymond91125 commented 2 years ago

@ValWood I guess the question is where the process "siderophore-dependent iron import" starts. I think it does not include the exporting of iron-free siderophore from the cell.

ValWood commented 2 years ago

I am not sure whether the export would be part of the pathway, or causally upstream. Go does not have good rules about this. @pgaudet ?

raymond91125 commented 2 years ago

siderophore transmembrane transport has the def "The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, from one side of a membrane to the other, by means of some agent such as a transporter or pore." It does not exclude any direction or membrane per se. Perhaps we can add the relationship siderophore-dependent iron import has_part siderophore transmembrane transport.

ValWood commented 2 years ago

Here what I wanted was an MF term to describe the activity of the ferrated siderophore.

(i.e siderophore-iron transmembrane transporter activity or ideally plasma membrane siderophore-iron transmembrane transporter activity

that could be part of both

GO:0033214 | siderophore-dependent iron import into cell and siderophore transmembrane transport

raymond91125 commented 2 years ago

@ValWood both of the part of relationships are in with my last commit https://github.com/geneontology/go-ontology/commit/17ecc9dd4842cf8ca135aa13ecb600549ea1ce14

raymond91125 commented 2 years ago

closed for now. thanks.