ntr nucleolus transport (was inc children nucleocyto...)

[gocentral]

The paper I am reading (PMID:16251348) implies that the process nucleocytoplasmic transport only includes protein import and mRNA export, and not the assembly and export of pre-ribosomal complexes from the nucleolus.

This seems to make sense, so it means that a number of the children are incorrect. I can also ask an expert to clarify.

Val

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/3277":https://sourceforge.net/p/geneontology/ontology-requests/3277

[gocentral]

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huh? I didn't get any sense that that paper tries to define nucleocytoplasmic transport, let alone that it should exclude the export of assembled (pre-) ribosomal subunits. Also, at present ribosome assembly isn't under nucleocytoplasmic transport in GO (tho ribosome export from nucleus has paths back to both ribosome biogenesis and nucleocytoplasmic transport).

I skimmed through the paper pretty quickly, so I'll leave this item open in case I missed something. But my initial impression is that there's nothing wrong with the GO terms and relationships.

m

Original comment by: mah11

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the paper refers to nuclear-cytoplasmic transport (rather than nucleocytoplasmic transport) in the last paragraph of "Grn is required for optimal growth"In the very last bit of the para (which is at the beginning of page 467)it says

nuclear-cytoplasmic (which I am assuming means the same as nulceocytoplasmic although it isn't a synonym)transport (protein import and RNA export)

but it appears to exclude export of the pre ribosomal complex from the nucleolus from this, because they infer that this particular GTPase is not involved in nuclear cytoplasmic transport BUT IS involved in ribosome export. This is is inconsistent with our ontology structure. an annotation to nucleaocytoplasmic transport would be implicit based on parentage)

maybe nucleocytoplasmic shuttling ( a narrower than synonym)=nucleocytoplasmic transport refers only to the system dependent on the karyopherin/importin family of cargo receptors. Shelly Sazer will know, keep this open and i'll ask her when we get back.

Val

Original comment by: ValWood

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Export of pre-ribosomal complexes from the nucleus is indisputably nucleocytoplasmic transport, especially given how GO defines the latter (basically moving anything into or out of the nucleus)!

Do let us know what Shelley says about shuttling, though; maybe we'll need children of nucleocytoplasmic transport (instead of just a narrow synonym) to distinguish shuttling from whatever other mode of transport. It depends on whether there's a good definition for the 'other', i.e. not just 'not shuttling'.

And we can add 'nuclear-cytoplasmic transport' as as synonym for nucleocytoplasmic transport, even tho it's used much, much less (159 vs 3635 PubMed hits).

m

Original comment by: mah11

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OK, mailed Shelly,

Val

Original comment by: ValWood

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Shellys response (Midori, Shelly sent a note for you GO is informing the experts ;)

Val, I have now read the whole paper, and think that my first response to you was correct. I think this system is complicated because the ribosomes need to be completely and properly assembled in tne nucleolus before the move into the nucleoplasm, and unless that get to the nucleoplasm they cannot be exported through the nuclear pores to the cytoplasm. So although this GTPase prevents the enxport of a particular ribosomal protein from both the nucleolus and the nucleus, its direct effect is on rRNA processing and the lack of nuclear export is secondary to this defect.

But, it is true that movement from the nucleolus is not the same as nuclear-cytoplasmic transport.

Let me know if this makes sense and if I can be of further help.

Speaking of GO......

Please tell Midori that I was able to use AmiGO to win a controversy with a colleague over the use of a term in a paper I am writing with him! He wanted to refer to something in the nuclear envelope lumen as perinuclear. I knew that these were two distinct locations in the cell (although a Google search gave conflicting definitions) and AmiGO did a perfect job of differentiating and defining them, and warning about getting these terms mixed up--so thanks!!

Original comment by: ValWood

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just to confuse the thread, this was Shelleys previous e-mail

> In GO we have > > nucleocytoplasmic transport > def: The directed movement of molecules between the nucleus and the > cytoplasm. > nucleocytoplasmic shuttling ( a narrower than synonym) of > nucleocytoplasmic transport

I THINK OF SHUTTLING AS MORE A PROPERTY OF THE PROTEIN BEING TRANSPORTED THAN THE MECHANISM. A PROTEIN THAT SHUTTLES BETWEEN THE NUCLEUS AND THE CYTOPLASM IS BOTH IMPORTED AND EXPORTED FROM THE NUCLEUS, USING MECHANISMS THAT ARE THE SAME AS THOSE USED BY PROTEINS THAT ARE JUST IMPORTED OR JUST EXPORTED. SHUTTLING PROTEINS HAVE BOTH NLS AND NES SEQUENCES. SO THERE WOULD NEVER BE A TRANSPORT FACTOR IN VOLVED IN SHUTTLING PER SE, BUT THERE ARE LIKELY TO BE MANY CARGOES THAT SHUTTLE.

> > > My questions are > > 1, are nucleocytoplasmic transport and nuclear-cytoplasmic transport > equivalent? YES

> and is the current definition > > 2. is the defintion of nucleocytoplasmic transport accurate? YES > > 3. Should we create a term 'nucleocytoplasmic shuttling' as a child of > 'nucleocytoplasmic transport' to separate the gene products involved in > the Ran GTPase/ karypherin mediated nucloclutoplasmic transport? If so, > how would this be defined?

SEE ABOVE, I DON'T THINK THAT THESE CAN BE SEPARATED MECHANISTICALLY.

PERHAPS THERE SHOULD BE A DIFFERENT TERM, CALLED INTRANUCLEAR TRANSPORT, REFERRING TO DIRECTED MOVEMENT OF PROTEINS WITHIN THE NUCLEUS. THIS WOULD NOT BE A SUB-FAMILY (CHILD?) OF NUCLEOCYTOPLASMIC TRANSPORT, BUT WOULD BE AT AN EQUIVALENT LEVEL TO INTRACYTOPLASMIC TRANSPORT (IF THERE IS SUCH A TERM) DESCRIBING THE DIRECTED MOVEMENT OF PROTEINS WITHIN THE CYTOPLASM.

MORE LATER, SHELLEY

>

Original comment by: ValWood

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OK, those emails from Shelly do help me understand a bit more about nucleocytoplasmic transport and ribosomes. But I still don't see anything wrong with the GO terms and relationships - they all seem consistent with what Shelly says.

We don't have any terms referring to movement of ribosomes or pre- ribosomal complexes from the nucleolus to the nucleoplasm. I agree that if we did, they shouldn't be children of nucleocytoplasmic transport.

m

Original comment by: mah11

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No you are right. The gene I am annotating is blocked at the export from the nucleolus/nucleoplasm step, so this term would be useful. I agree the current terms are correct though...

Original comment by: ValWood

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OK, added nucleolus to nucleoplasm transport GO:0032066

is that it for this item?

Original comment by: mah11

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yep tks

Original comment by: ValWood

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yay, closing!

Original comment by: mah11

[gocentral]

• labels: --> New term request
• assigned_to: nobody --> gomidori
• summary: inc children nucleocytoplasmic transport --> ntr nucleolus transport (was inc children nucleocyto...)
• milestone: --> 224410
• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11