Missing parent: GO:0033214 siderophore-dependent iron import into cell

[ValWood]

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

GO:0033214 siderophore-dependent iron import into cell

• New superclass (parent) suggested

GO:0044718 siderophore transmembrane transport

[ValWood]

It seems that iron-siderophore uptake can be both vesicle-mediated transport and via transmembrane transporters.

However, since the siderophore system is only used for uptake, should

GO:0044718 siderophore transmembrane transport
be part_of GO:0033214 siderophore-dependent iron import into cell

(O:0015343 siderophore-iron transmembrane transporter activity
is already part_of

In fact, this looks slightly odd:

Why isn't

siderophore-dependent iron import into cell
A process in which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, excreted by a cell; the iron-siderophore complex is then transported into the cell by specific cell surface receptors. PMID:16963626

part_of siderophore transport?

Suggest

• GO:0033214  siderophore-dependent iron import into cell
  is_a
  GO:0015891 siderophore transport

• GO:0044718 siderophore transmembrane transport
  is_a
  GO:0033214  siderophore-dependent iron import into cell

• Revise/clarify definition
  GO:0033214 siderophore-dependent iron import into cell
  A process in which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, excreted by a cell; the iron-siderophore complex is then transported into the cell by specific cell surface receptors. PMID:16963626
  ->
  A process in which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, the iron-siderophore complex is then transported into the cell by specific cell surface receptors or transmembrane transporters. PMID:16963626

[ValWood]

@pgaudet let me know if this sound OK, no hurry

[pgaudet]

This branch is odd.

As discussed yesterday, we should obsolete 'siderophore transport' since it doesn't describe the mechanism.
As it is, these 3 highlighted terms seem redundant:

However, do we need 'siderophore export'? I suppose the empty siderophore must be exported to get the iron? I am not sure how that part works. Other the 3 other terms, at least based on their parentage, seem redundant to me.

What do you think ?

[ValWood]

Export seems to be tm transport too, at least in some systems:
https://pubmed.ncbi.nlm.nih.gov/23431276/
These results identified MmpS4/MmpL4 and MmpS5/MmpL5 as siderophore export systems in Mtb and revealed that the MmpL proteins transport small molecules other than lipids. MmpS4 and MmpS5 resemble periplasmic adapter proteins of tripartite efflux pumps of Gram-negative bacteria, however, they are not only required for export but also for efficient siderophore synthesis.

https://pubmed.ncbi.nlm.nih.gov/14638426/
The csbX gene of Azotobacter vinelandii was regulated in an iron-repressible manner from a divergent promoter upstream of the catecholate siderophore biosynthesis (csb) operon and was predicted to encode an efflux pump of the major facilitator superfamily. Other proteins that were most similar to CsbX were encoded by genes found in the catecholate siderophore biosynthesis operons of Aeromonas hydrophila and Stigmatella aurantiaca. Inactivation of csbX resulted in 57-100% decrease in the amount of catecholates released when compared to the wild-type in iron-limited medium. CsbX was most important for the export of the high affinity chelator protochelin with the majority of the catecholates released by csbX mutants being the protochelin intermediates azotochelin and aminochelin.

https://pubmed.ncbi.nlm.nih.gov/21306443/
Results establish that EntS and IroC mediate specific export of catecholate siderophores and the role of these exporters for ExPEC virulence is contingent on enterobactin synthesis, which is not required when other siderophores like aerobactin are functional.

[ValWood]

The process of siderophore transport system also includes a secreted ferric reductase which solubilizes /reduces the iron from Fe 3+ to Fe 2+

[ValWood]

This was the problem I was trying to solve.
I annotated to

I expected the IBA to be covered by this IMP annotation.

[pgaudet]

The issue is that GO:0044718 siderophore transmembrane transport does not imply a directionality, while GO:0033214 siderophore-dependent iron import into cell does.

What I would like for transport is the undirected reactions be MFs, and the directed ones be BPs. If we dont know the biological consequence of the transport reaction, can we really say we know the BP ?

Does that address your question?

Thanks, Pascale

[ValWood]

I'm not sure.

I was requesting that "siderophore-dependent iron import into cell"
was a descendant of
"siderophore transmembrane transport"
The directionality of the parent should not matter.

If this is not possible, it should still go to
"siderophore transport"

[ValWood]

I just remembered the history. It might be something to do with siderophores being transported when they are not iron-associated"

[ValWood]

However that does not make sense either because

GO:0015891 siderophore transport
has
siderophore-iron transport | exact

(if this is correct, we should make use the more explicit label)

[pgaudet]

See also #23199

it seems we are going back and forth?

[ValWood]

OK, I have removed waiting for feedback. The current organization is clearly incorrect (because siderophore transport is a descendant of iron ion transport), so the previous ticket didn't fix things.
I have enough info to make a more complete proposal.

[ValWood]

This is out of date (and confused). Proposed solution now in #29742