ntr: term for directed movement of membrane proteins from ciliary membrane back to plasma membrane

[gocentral]

Hi,

I am reading PMID:22139371 and want to be able to represent the process of transporting ciliary membrane proteins back to the plasma membrane. For example, in this paper, they say this:

We stained mouse embryonic fibroblast (MEF) cells from WT and Bbs3−/− mice with antiacetylated tubulin and anti-Smo. Smo was accumulated inside cilia in 30–40% of Bbs3−/− MEF cells

Thus, the Bbs3 (aka Arl6) protein is involved in removing membrane proteins from the ciliary membrane by transporting them back to the plasma membrane. To just annotate to "protein localization of plasma membrane" doesn't seem sufficient since this process is very specific to removal from the ciliary membrane. I'm not sure exactly what to call it though. Would this work?

"protein localization to plasma membrane from ciliary membrane" Def: "A process in which a protein is transported to the plasma membrane from the ciliary membrane." is_a "protein localization to plasma membrane" GO:0072659

Also, I notice that there is a term for "intermembrane transport", which also seems like a valid is_a parent for this proposed new term, if we're still allowing multiple is_a parents.

Looking at this area, I also realize that I think it would be good to have this new term: term: protein localization to ciliary membrane - GO:new is_a: protein localization to membrane - GO:0072657 Def: A process in which a protein is transported to, or maintained in, a specific location in the ciliary membrane.

Also, why is "protein localization to basolateral plasma membrane" GO:1903361 not an is_a child of "protein localization to plasma membrane" GO:0072659?

thanks,

-Karen

Reported by: krchristie

Original Ticket: geneontology/ontology-requests/11158

[gocentral]

Hi Karen,

Wrt your last question

why is "protein localization to basolateral plasma membrane" GO:1903361 not an is_a child of "protein localization to plasma membrane" GO:0072659?

This should be fixed when we get to this related request:

https://sourceforge.net/p/geneontology/ontology-requests/11090/

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• labels: --> Cilia/flagella
• assigned_to: Paola Roncaglia

Original comment by: jl242

[gocentral]

Hi Karen,

I started with adding this term via TG (I used the 'protein_localization_to' template, see 'View in tree' and expand 'localization'):

[Term] id: GO:1903441 name: protein localization to ciliary membrane namespace: biological_process def: "A process in which a protein is transported to, or maintained in, a location within a ciliary membrane." [GO_REF:0000087, GOC:krc, GOC:TermGenie, PMID:22139371] synonym: "protein localisation in ciliary membrane" EXACT [GOC:TermGenie] synonym: "protein localisation to ciliary membrane" EXACT [GOC:TermGenie] synonym: "protein localization in ciliary membrane" EXACT [GOC:TermGenie] is_a: GO:0061512 {is_inferred="true"} ! protein localization to cilium is_a: GO:0072659 {is_inferred="true"} ! protein localization to plasma membrane intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0060170 ! ciliary membrane relationship: has_target_end_location GO:0060170 {is_inferred="true"} ! ciliary membrane

I'm looking into the rest of your request and will update soon.

Thanks,

Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Karen,

Would this work?

GO:NEW protein transport from ciliary membrane to plasma membrane

'transport' is a descendant of 'localization' (and 'establishment of localization') so this new term would be more specific than the one you suggest.

The new term would be structured similarly to this one, in terms of logical definitions: (but not identical, see below)

[Term] id: GO:0006611 name: protein export from nucleus def: "The directed movement of a protein from the nucleus into the cytoplasm." [GOC:jl] is_a: GO:0006886 ! intracellular protein transport is_a: GO:0051168 ! nuclear export is_a: GO:1902582 {is_inferred="true"} ! single-organism intracellular transport intersection_of: GO:0006810 ! transport intersection_of: exports CHEBI:36080 ! protein intersection_of: has_target_end_location GO:0005737 ! cytoplasm intersection_of: has_target_start_location GO:0005634 ! nucleus

As for the 'intermembrane transport' parent, that would be ok except for one not-so-small detail. I think we need to relax both the textual and logical definitions of 'intermembrane transport' and its ancestors:

[Term] id: GO:0046909 name: intermembrane transport namespace: biological_process def: "The directed movement of substances between the intracellular membranes of a cell, for example, the transfer of glycolipids from the endoplasmic reticulum to other cellular membrane structures in which they reside." [GOC:ai, PMID:10671554] is_a: GO:1902582 {is_inferred="true"} ! single-organism intracellular transport

As we resolved, 'cilium' is definitely not intracellular, so 'ciliary membrane' would not be considered an intracellular membrane. For 'intermembrane transport' to apply to the ciliary membrane (which would sound quite legitimate to me), the def. should say

"The directed movement of substances between any membrane of a cell, (...)"

The parent 'single-organism intracellular transport' has stanza:

[Term] id: GO:1902582 name: single-organism intracellular transport def: "An intracellular transport which involves only one organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie] is_a: GO:0044765 {is_inferred="true"} ! single-organism transport is_a: GO:0046907 {is_inferred="true"} ! intracellular transport intersection_of: GO:0046907 ! intracellular transport intersection_of: bearer_of PATO:0002487 ! single organismal process quality

And going up the graph:

[Term] id: GO:0046907 name: intracellular transport def: "The directed movement of substances within a cell." [GOC:ai] is_a: GO:0006810 {is_inferred="true"} ! transport is_a: GO:0051649 {is_inferred="true"} ! establishment of localization in cell intersection_of: GO:0006810 ! transport intersection_of: has_target_end_location GO:0044464 ! cell part intersection_of: has_target_start_location GO:0044464 ! cell part _intersection_of: occursin GO:0005622 ! intracellular intersection_of: results_in_transport_across GO:0044464 ! cell part

The problem lies here:

[Term] id: GO:0005622 name: intracellular def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] is_a: GO:0044464 ! cell part

Possible solutions:

• create a term for 'single-organism cellular transport' with parent 'cellular transport' that occurs_in 'cell' rather than 'intracellular'; the existing terms 'single-organism intracellular transport' and 'intracellular transport' would be placed as their children;
• change existing 'single-organism intracellular transport' and 'intracellular transport' to occur in 'cell' rather than 'intracellular', but this might be lexically confusing? Unless we rename them 'cellular' rather than 'intracellular'?
• others?

Other existing terms seem to be affected by the same issue, e.g.:

[Term] id: GO:0006605 name: protein targeting def: "The process of targeting specific proteins to particular membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif." [GOC:ma] comment: Note that protein targeting encompasses the transport of the protein to the specified location, and may also include additional steps such as protein processing. is_a: GO:0006886 ! intracellular protein transport is_a: GO:1902582 {is_inferred="true"} ! single-organism intracellular transport

The textual def. would not exclude the ciliary membrane, but the logical def. of the parent would.

I'll consult with the other editors.

Thanks, Paola

P.S. I also noticed this one:

[Term] id: GO:0071693 name: protein transport within extracellular region def: "The directed movement of proteins in the extracellular region, by means of some agent such as a transporter or pore." [GOC:mah] is_a: GO:0015031 ! protein transport is_a: GO:0035592 ! establishment of protein localization to extracellular region is_a: GO:0044765 ! single-organism transport is_a: GO:0071692 {is_inferred="true"} ! protein localization to extracellular region created_by: midori creation_date: 2010-02-25T04:02:35Z

I presume the 'pore' bit in the def. was added mistakenly in copy-paste and should be removed.

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

Your suggestion to create: GO:NEW protein transport from ciliary membrane to plasma membrane

seems fine to me.

Everything else you've said about the logical and definition issues with the term "intermembrane transport" makes sense to me.

thanks,

-Karen

Original comment by: krchristie

[gocentral]

Hi Karen,

I added GO:1903445 protein transport from ciliary membrane to plasma membrane using the TG template called 'chemical_transport_from_to' ('View in tree', then expand 'transport'), and CHEBI:36080 ! protein for the logical definition. The full stanza is below for your reference. More later on the remaining issues...

Paola

[Term] id: GO:1903445 name: protein transport from ciliary membrane to plasma membrane namespace: biological_process def: "The directed movement of protein from ciliary membrane to plasma membrane." [GO_REF:0000078, GOC:krc, GOC:TermGenie, PMID:22139371] is_a: GO:0015031 {is_inferred="true"} ! protein transport is_a: GO:0044765 {is_inferred="true"} ! single-organism transport is_a: GO:0072659 {is_inferred="true"} ! protein localization to plasma membrane is_a: GO:0090002 {is_inferred="true"} ! establishment of protein localization to plasma membrane intersection_of: GO:0006810 ! transport intersection_of: has_target_end_location GO:0005886 ! plasma membrane intersection_of: has_target_start_location GO:0060170 ! ciliary membrane intersection_of: transports_or_maintains_localization_of CHEBI:36080 ! protein relationship: has_target_end_location GO:0005886 {is_inferred="true"} ! plasma membrane relationship: has_target_start_location GO:0060170 {is_inferred="true"} ! ciliary membrane relationship: transports_or_maintains_localization_of CHEBI:36080 {is_inferred="true"} ! protein

Original comment by: paolaroncaglia

[gocentral]

• status: open --> open-accepted

Original comment by: paolaroncaglia

[gocentral]

On second thought, I'll leave the def. of GO:0071693 as is because 'extracellular region' is "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." so we can't completely rule out involvement of pores if they belong to a host cell.

Original comment by: paolaroncaglia

[gocentral]

Leaving this item open until we resolve the 'intracellular' issue. I will then evaluate if 'intermembrane transport' is a further appropriate parent for 'protein transport from ciliary membrane to plasma membrane'.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Edited GO:0046909 'intermembrane transport': moved it up to be is_a GO:0044765 'single-organism transport'; relaxed its def. to read: "The directed movement of substances between any membrane of a cell, including the plasma membrane and its regions."; added def. comment: "Examples of intermembrane transport are the transfer of glycolipids from the endoplasmic reticulum to other cellular membrane structures in which they reside, and the movement of proteins between regions of the plasma membrane (where one region could be the ciliary membrane).";

made 'protein transport from ciliary membrane to plasma membrane' is_a 'intermembrane transport'.

Added new term for future use: GO:0097653 unencapsulated part of cell is_a cell part has_part intracellular has_part plasma membrane The part of a cell encompassing the intracellular environment and the plasma membrane; it excludes any external encapsulating structures. GOC:curators

Closing now, thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• labels: Cilia/flagella --> Cilia/flagella, New term request, Other term-related request
• status: open-accepted --> closed-accepted

Original comment by: paolaroncaglia