GO:0005487 - nucleocytoplasmic transporter activity parent

[ValWood]

GO:0005487 nucleocytoplasmic transporter activity is a "molecular carrier activity"

not "protein transporter activity"

see https://github.com/geneontology/go-ontology/issues/14331 https://github.com/geneontology/go-ontology/issues/14221

[pgaudet]

@rachhuntley let me know if this addresses the point you raised.

Thanks, Pascale

[bmeldal]

Typo:

GO:0005049 : ...to mediate transport of a the cargo through the nuclear pore, from the nuclear to the cytoplasm.

should be nucleUS

(Sorry, I'm late to the part due to time off)

[pgaudet]

Hi @bmeldal Thanks for reporting this ! In fact I meant 'nuclear lumen'; is that OK ?

I also added logical definitions as follows:

• GO:0140142 nucleocytoplasmic carrier activity molecular carrier activity part_of some nucleocytoplasmic transport

• GO:0061608 nuclear import signal receptor activity nucleocytoplasmic carrier activity part_of some import into nucleus

• GO:0005049 nuclear export signal receptor activity nucleocytoplasmic carrier activity part_of some nuclear export

Thanks, Pascale

[ValWood]

Hi Pascale, it should be nucleus, not nuclear lumen. The cargo is moving from the nucleus to the cytoplasm or vice versa but it isn't crossing the "nuclear envelope lumen"

This seems "unimportant" but if you think of the nuclear lumen as continuous with the ER it makes more sense why we need to keep these separate. The nuclear lumen is continuous with the ER and the cytoplasm is continuous with the nucleus.

There are very precise ways to get into the lumen. I think this makes it clearer than my previous explanations as it shows the broader context, not only the nuclear pore:

[mah11]

Nuclear lumen =/= nuclear envelope lumen, and I don't see a problem with using nuclear lumen in this def.

[ValWood]

Ah OK, I never see the use of this phrase only "nuclear envelope lumen" ignore.

[pgaudet]

Thanks for the clarification @mah11 I was trying to say this the cargo does inside the nucleus, and not to the envelope, for example.

All good ?

Thanks, Pascale

[ValWood]

Is it really a "lumen"? I don't find any reference to "nuclear lumen" except in GO and a "lumen" is a "cavity within a tubular structure"

[pgaudet]

well - that's another story. It was there so I have been using it !

[ValWood]

I think it would be confusing to use just "lumen" Everything I can find about "nuclear lumen" is referring to "nuclear envelope lumen.

If we use lumen it will become even more difficult to keep this from being confused with transmembrane transport. Could you use from the "nucleoplasm" if you don't want to use from the "nucleus" ?

[mah11]

"Lumen" is not restricted only to tubular structures - definitions I've found, including OED, say "The central cavity of a tubular or other hollow structure in an organism or cell."

"Nuclear lumen" doesn't seem to be a commonly used phrase, and I don't really care whether it stays in the GO definition or not, but its meaning is unambiguous.

[ValWood]

It would be good to find an example of it's use in this context if we keep it.

[ValWood]

Note that last week "nucleocytoplasmic transporter" reverted to being a transporter not a carrier. Although people call it a carrier, it isn't a carrier in the GO sense, it's a transporter.

@pgaudet can you link this to the ticket documenting the change, I can't find it. I'm still a little confused by exactly what classifies as "carrier" do it would be good to have a trail for this.

[pgaudet]

There was no ticket yet - thanks for the reminder ! Here: https://github.com/geneontology/go-ontology/issues/17399