BCR translocation

[gocentral]

Hi

PMID:11313396

I am annotating human CD24 (P25063) after CD24 crosslinking, the B-cell receptor on the PM moves into the GEM domain and is therefore found experimentally in the GEM membrane fraction (see previous SF request).

Can I have a term for BCR translocation...

>B cell receptor membrane translocation >> B cell receptor membrane translocation to GEM domain (?) Exact Synonym:BCR translocation

or something like that...not sure of parentage..

cheers

Evelyn

Reported by: ecamon

Original Ticket: "geneontology/ontology-requests/4476":https://sourceforge.net/p/geneontology/ontology-requests/4476

[gocentral]

Logged In: YES user_id=436423 Originator: NO

It looks like the crosslinking of either BCR or CD24 is an experimental technique using antibodies -- does it correspond to any naturally occurring event?

Also, is it good evidence that CD24 plays a direct role in making BCR move?

(Sorry, I'm not very familiar with this type of experiment ...)

m

Original comment by: mah11

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Hi Midori,

Thanks for looking at this... Ok they worked on Burkitt Lymphoma cells which of course are tumor cells BUT the author states that they used them because they retain the properties of normal germinal centre B cells. Secondly CD24 cross linking is just a way of using Ab to experimentally mimic ligand binding to cd24, they did indeed show that stimulation of cd24 in this way affected the distribution of the B cell receptor mu heavy chain into the GEM domain/lipd raft(pp5573). BCR cross linking also caused BCR translocation but not into the GEM domain, only CD24 cross linking caused that....so i think thats worth capturing.

It is quite difficult in the literature to find papers to curate cd24 so i would really like this term..could see what alex's thinks but receptor translocation to certain parts of a membrane during activation represents a common and normal process.

Evelyn

Original comment by: camon

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I think the use of BL cells as a model for B cell behavior is quite common. Also, antibody cross-linking of surface receptors is both a common and proven method for studying signaling pathways in mammalian cells as well as the behavior of surface molecules, used probably in tens of thousands of papers in immunology and other fields.

Also, translocation of the TCR into lipid raft domains upon T cell activation is well described, and I know that the BCR signals and moves in similar ways. I have no problem with this term at all and probably we will need similar terms to describe the movement of other cell surface receptors, such as the TCR, ICAM-1, CD45, and many others whose movements into or out of lipid rafts and the immunological synapse have been described in great precision.

As for parentage, I think "protein transport ; GO:0015031" might fit well, although "membrane organization and biogenesis ; GO:0016044".

In fact this is what I propose:

protein transport ; GO:0015031 --% protein transport within lipid bilayer ; GO:NewTerm ----% B cell receptor transport within lipid bilayer ; GO:NewTerm ------% B cell receptor transport into lipid raft ; GO:NewTerm --------% B cell receptor transport into immunological synapse ; GO:NewTerm

membrane organization and biogenesis ; GO:0016044 --% protein transport within lipid bilayer ; GO:NewTerm ----% B cell receptor transport within lipid bilayer ; GO:NewTerm ------% B cell receptor transport into lipid raft ; GO:NewTerm --------% B cell receptor transport into immunological synapse ; GO:NewTerm

I would love to write the definitions now and find additional references, but I am tired and need to go to bed. If you like this approach, I could write up some definitions the morning or provide constructive criticism to any either of you write.

Thanks,

Alex

Original comment by: addiehl

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Hi Alex,

Your parentage sounds perfect to me. Hope you have a good sleep.

Evelyn

Original comment by: ecamon

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Ev & Alex,

Many thanks to both of you for the information, and for reassuring me about the proposed term! I have no objection to the terms and parentage suggested.

Would it be of any use to include more generic terms for 'receptor transport within lipid bilayer' or '...into lipid raft'?

i.e. protein transport ; GO:0015031 --% protein transport within lipid bilayer ; GO:NewTerm ----% receptor transport within lipid bilayer ; GO:NewTerm ------% B cell receptor transport within lipid bilayer ; GO:NewTerm --------% B cell receptor transport into lipid raft ; GO:NewTerm ----------% B cell receptor transport into immunological synapse ; ------% receptor transport into lipid raft ; GO:NewTerm --------% B cell receptor transport into lipid raft ; GO:NewTerm ----------% B cell receptor transport into immunological synapse ; GO:NewTerm

Alex - I've drafted some definitions for your constructive criticism (it's the least I could do, after you stayed up so late to comment). The additional references would be most welcome, especially for the more generic terms ... unless you think the simplistic standardized ones I've filled in will do. I've also had a stab at some synonyms, which would also benefit from your attention.

[Term] id: GO:NewTerm1 name: protein transport within lipid bilayer namespace: biological_process def: The directed movement of a protein within a lipid bilayer. [GOC:mah] synonym: "protein translocation within membrane" EXACT [] is_a: GO:0015301 is_a: GO:0016044

[Term] id: GO:NewTerm2 name: receptor transport within lipid bilayer namespace: biological_process def: The directed movement of a receptor within a lipid bilayer. [GOC:mah] synonym: "receptor translocation within membrane" EXACT [] is_a: GO:NewTerm1

[Term] id: GO:NewTerm3 name: B cell receptor transport within lipid bilayer namespace: biological_process def: The directed movement of a B cell receptor within a lipid bilayer. [GOC:mah] synonym: "B cell receptor translocation within membrane" EXACT [] synonym: "BCR translocation within membrane" EXACT [] synonym: "BCR transport within lipid bilayer" EXACT [] is_a: GO:NewTerm2

[Term] id: GO:NewTerm4 name: receptor transport into lipid raft namespace: biological_process def: The directed movement of a receptor into a lipid raft. [GOC:mah] synonym: "receptor translocation into lipid raft" EXACT [] is_a: GO:NewTerm1

[Term] id: GO:NewTerm5 name: B cell receptor transport into lipid raft namespace: biological_process def: The directed movement of a B cell receptor into a lipid raft. [GOC:mah] synonym: "B cell receptor translocation into lipid raft" EXACT [] synonym: "BCR translocation into lipid raft" EXACT [] synonym: "BCR transport into lipid raft" EXACT [] is_a: GO:NewTerm3 is_a: GO:NewTerm4

[Term] id: GO:NewTerm6 name: B cell receptor transport into immunological synapse namespace: biological_process def: The directed movement of a B cell receptor into an immunological synapse. [GOC:mah] synonym: "B cell receptor translocation into immunological synapse" EXACT [] synonym: "BCR translocation into immunological synapse" EXACT [] synonym: "BCR transport into immunological synapse" EXACT [] is_a: GO:NewTerm5

midori

Original comment by: mah11

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Midori,

I like your definitions. I'm wondering if the receptor transport term is needed -- I'm trying to think of a cell surface protein that is not a receptor, but that might be subjected to movement. Of course these terms are not limited to the plasma membrane (which is fine by me).

Anyway, I'll leave the final decision up to you.

Thanks,

Alex

Original comment by: addiehl

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Good question. Obviously there are plenty of membrane proteins that aren't receptors, but I really don't know if their locations within the membrane are controlled as specifically as receptor location.

Another option is to include 'receptor transport within membrane' as a narrow synonym of 'protein transport within membrane', rather than as a separate term. Better, worse, indifferent?

m

Original comment by: mah11

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I think the synonym approach works for now -- we can always add a specific term later for 'receptor transport within membrane' if necessary. No need to add an extra layer if we will never use it.

-- Alex

Original comment by: addiehl

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Hi Guys,

This is again related to lipid rafts so I thought Id add here:

PMID:16390867 (Mouse paper on CD24 and Chemokine receptor (CXCR4)

CD24 alters CXCR4 lipid raft residence

what term could we use here?

'Chemokine receptor transport out of the lipid raft'

ev?

Original comment by: ecamon

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Evelyn and Midori,

I can see that we need 'protein transport into lipid raft' and 'protein transport out of lipid raft', plus a specific term for chemokine receptors. CD45 is another protein that is moved out of lipid rafts upon T cell activation, so there will be future use for the 'out of' term too.

How about this?

protein transport ; GO:0015031 --% protein transport within lipid bilayer ; GO:NewTerm ----% protein transport into lipid raft ; GO:NewTerm ------% B cell receptor transport into lipid raft ; GO:NewTerm --------% B cell receptor transport into immunological synapse ; GO:NewTerm ----% protein transport out of lipid raft ; GO:NewTerm ------% chemokine receptor transport out of lipid raft ; GO:NewTerm ----% B cell receptor transport within lipid bilayer ; GO:NewTerm ------% B cell receptor transport into lipid raft ; GO:NewTerm --------% B cell receptor transport into immunological synapse ; GO:NewTerm

Cheers,

Alex

Original comment by: addiehl

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OK, I've added these terms, using the defs I proposed (or obvious edits thereof); please check!

protein transport within lipid bilayer GO:0032594 B cell receptor transport within lipid bilayer GO:0032595 protein transport into lipid raft GO:0032596 B cell receptor transport into lipid raft GO:0032597 B cell receptor transport into immunological synapse GO:0032598 protein transport out of lipid raft GO:0032599 chemokine receptor transport out of lipid raft GO:0032600 chemokine receptor transport within lipid bilayer GO:0032606

If all is well, I'll close this item. Thanks again for the help, m

Original comment by: mah11

[gocentral]

• status: open --> open-accepted

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PAINT
• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

• status: open-accepted --> closed-accepted

Original comment by: mah11