NTR: [paracellular transport at tight junction]

[nnouspikel]

Dear GO curators,

I would like to discuss with you the possibility of creating a biological process term for epithelial paracellular transport at tight junctions; it’s relevant to channel-forming claudins https://www.tcdb.org/browse.php https://www.tcdb.org/search/index.php?query=claudin%202&type=system review: PMID:30665499; PMID:28869648; PMID:28605828; PMID:21365189

new GO term: paracellular transport at tight junction definition: The movement of solutes through a paracellular channel formed in the tight junction strands. child of GO:0006810 transport synonyms: paracellular epithelial permeability; pore pathway; tight junction-mediated paracellular transport

Maybe we can create the related molecular function term as well: new GO term: paracellular channel activity definition: A pore channel activity that enables size- and charge-selective transport of solutes through a tight junction barrier across the epithelium. child of GO:0022842 narrow pore channel activity PMID:21365189 synonym: claudin pore

Thank you for your help and all the best, Nevila Hyka-Nouspikel

[pgaudet]

Hi Nevila,

Would it be a sibling of these terms:

• GO:0010496 intercellular transport
• • GO:1990349 gap junction-mediated intercellular transport
• • GO:0010497 plasmodesmata-mediated intercellular transport
• • GO:0110077 vesicle-mediated intercellular transport

?

Thanks, Pascale

[nnouspikel]

Hi Pascale,

Yes GO:0010496 intercellular transport is the most appropriate parent term.

Thanks a lot, Nevila

[ValWood]

I was curious what it is Google:

https://pubmed.ncbi.nlm.nih.gov/12609869/ "Unlike conventional ion channels, which mediate ion transport across lipid bilayers, the tight junction channels must orient parallel to the plane of the plasma membranes to support paracellular ion movements"

it seems the critical differentia is "facilitates the transport of ions between separate extracellular compartments"

see image in https://www.researchgate.net/publication/314233504_Nanoformulation_and_administration_of_PUFA-rich_systems_for_applications_in_modern_healthcare/figures?lo=1

I think we should just have "paracellular transport" for process (exclude location at ticght junction, can be captured with extension, and MF "tight junction ion channel"

would be more flexible for other types of paracellular transport (which needs to be defined somehow as between cells not inter cells

[nnouspikel]

Thank you Val.

"paracellular transport" for process and "paracellular/tight junction channel activity" for molecular function – sounds all right, but up to you to decide; note that tight junction channels are permeable to uncharged molecules like water

All the best, Nevila

[pgaudet]

So, gap junction transport is 'intercellular' and tight junctions is paracellular?

What is paracellular ? It seems synonymous with intercellular https://en.wikipedia.org/wiki/Paracellular_transport Should we replace 'intercellular' with 'paracellular'?

[ValWood]

They are different:

Intercellular: Intercellular communication or processes occur within the cell itself or involve direct interactions between cells.

Paracellular: This term refers to the movement of substances between cells through the space that exists between adjacent cells. it's the passage of molecules or ions through the intercellular space without actually passing through the cell membrane.

Paracellular isn't going in

[nnouspikel]

I agree, they are different. Here is a schematic depicting gap and tight junction channels: https://ars.els-cdn.com/content/image/1-s2.0-S0022283614005713-gr4_lrg.jpg (PMID:25451028)

[raymond91125]

[raymond91125]

I am not sure what the parent should be for MF "tight junction channel activity". It cannot be a child of GO:0015267 channel activity because it's not of transmembrane transport; or a child of GO:0005215 transporter activity because it's not transporting in/out/between cells (I think between here means inter cellular).

[raymond91125]

+[Term] +id: GO:0160184 +name: paracellular transport +namespace: biological_process +def: "The directed movement of substance through the space in between adjacent cells, rather than through the cells themselves." [PMID:28452575, WIki:Paracellular_transport] +is_a: GO:0006810 ! transport +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27621" xsd:anyURI +created_by: rynl +creation_date: 2024-04-29T23:13:30Z

[nnouspikel]

Thank you very much for creating GO:0160184.

Regarding the parent of MF "tight junction channel activity" , perhaps we can extend the definition of GO:0005215 transporter activity to include the paracellular transporter activity which occurs ‘in between’ cells.

here are a few definitions according to experts Paracellular transport refers to transport that occurs in between cells, passing through an intercellular shunt pathway. https://pubmed.ncbi.nlm.nih.gov/28452575/

Paracellular transport: passive movement of water and solutes through the space between adjacent cells (paracellular space) https://pubmed.ncbi.nlm.nih.gov/20936941/

[raymond91125]

GO:0005215 transporter activity DEF "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells". Should we change that to "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or through the space in between adjacent cells."? The original definition was referenced to GOC:dgf, GOC:ai. Can we consult them? @pgaudet

[raymond91125]

@pgaudet Do you think we need to revise the definition of GO:0005215 transporter activity to accommodate "paracellular tight junction channel activity"?

[pgaudet]

I would add this as a direct child of transporter activity:

[pgaudet]

I see the definiton is "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells."

Change to "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, across or in between cells."

[raymond91125]

+[Term] +id: GO:0160187 +name: paracellular tight junction channel activity +namespace: molecular_function +def: "Enables size- and charge-selective transport of solutes through a tight junction barrier paracellularly, across the epithelium." [PMID:30665499] +synonym: "claudin pore" EXACT [] +is_a: GO:0005215 ! transporter activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27621" xsd:anyURI +created_by: rynl +creation_date: 2024-05-14T00:31:01Z

[raymond91125]

Please let me know if anything else is needed. Thanks.

[pgaudet]

Look good!

[nnouspikel]

Thank you!