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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR:? mechanoreceptor activity #18636

Closed ValWood closed 2 years ago

ValWood commented 4 years ago

I can't find a term for mechanoreceptor

although lots of terms mention mechanoreceptors? GO:0042490 mechanoreceptor differentiation 7,301 annotations GO:0045631 regulation of mechanoreceptor differentiation 503 annotations GO:0045632 negative regulation of mechanoreceptor differentiation 270 annotations GO:0045633 positive regulation of mechanoreceptor differentiation 78 annotations

as a type of transmembrane signalling receptor?

ValWood commented 4 years ago

For yeast we have stretch receptors to detect changes in cell wall integrity

ref https://www.ncbi.nlm.nih.gov/pubmed/31404395?dopt=Abstract

but I guess would encompass sound and other sensory receptors?

ValWood commented 4 years ago

note to self wsc1

hdrabkin commented 4 years ago

Will need term definition; references, is parent (unless sure they would always be type of transmembrane signalling receptor).

ValWood commented 4 years ago

Ah I think the "mechanoreceptor" in the terms above is different. It seems to be referring to a cell type. Is that correct?

ValWood commented 4 years ago

I wasn't sure if there was a term already but I couldn't find it. The mechanoreceptors I am referring to are always TM receptors. Reference above.

I'll write a def based on this if nothing exists already.

ValWood commented 4 years ago

All the terms above are missing the word "cell" The children are all posterior lateral line neuromast hair cell differentiation inner ear receptor cell development etc

ValWood commented 4 years ago

Suggested def

Detecting with an external mechanical stimuli and transmitting a signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.

ValWood commented 4 years ago

and fix

GO:0042490 mechanoreceptor cell differentiation 7,301 annotations GO:0045631 regulation of mechanoreceptor cell differentiation 503 annotations GO:0045632 negative regulation of mechanoreceptor cell differentiation 270 annotations GO:0045633 positive regulation of mechanoreceptor cell differentiation 78 annotations

pgaudet commented 4 years ago

Can you add synonyms to either (or all) of those:

GO:0008381 mechanosensitive ion channel activity [is_a relation] GO:0043854 cyclic nucleotide-gated mechanosensitive ion channel activity [is_a relation] GO:0140135 mechanosensitive cation channel activity

Thanks, Pascale

ValWood commented 4 years ago

Ah right I thought something existed already. However, I want to annotate yeast wsc1 which isn't an ion channel. Some mechanoreceptors are ion channels and some aren't? These are like integrins https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6685044/figure/fig3/

ValWood commented 4 years ago

They are actually referred to as "sensors" rather than receptors. How do we differentiate between a sensor and a receptor?

pgaudet commented 4 years ago

We use the 'sensor activity' term ;)

However the most general one is 'small molecule sensor activity' ...?

pgaudet commented 4 years ago

How are integrins annotated ? I wonder if we need a separate activity or if we can add a synonym to an existing term.

pgaudet commented 4 years ago

OK in PAINT (PTHR23220) primary annotations are mostly to binding.

So we probably need that new term.

ValWood commented 4 years ago

one integrin

actin binding Source: BHF-UCL cadherin binding Source: BHF-UCL cell adhesion molecule binding Source: UniProtKB collagen binding involved in cell-matrix adhesion Source: UniProtKB coreceptor activity Source: UniProtKB fibronectin binding Source: UniProtKB integrin binding Source: GO_Central laminin binding Source: Ensembl metal ion binding Source: UniProtKB-KW protease binding Source: UniProtKB protein-containing complex binding Source: UniProtKB protein heterodimerization activity Source: UniProtKB virus receptor activity Source: UniProtKB-KW (plus more 81 total, mainly binding)

pgaudet commented 4 years ago

right :(

ValWood commented 4 years ago

EXP for pthr10082 | protein_coding_gene

krchristie commented 4 years ago

There are a lot of integrins. When I was trying to annotate some of them a while ago, I don't remember anything about mechanosensory activity. Looking at Wikipedia: https://en.wikipedia.org/wiki/Integrin seems consistent with the idea that different integrins do different things, so possibly not safe to associate mechanosensor activity generally with integrins.

I have come across mechanosensing numerous times at cilia meetings. I don't know if I've seen a really clear elucidation of how this is working, whether there is a receptor in the ciliary membrane (not sure I've ever seen that suggested at all), or whether it is some mechanical property of the cilium as a whole.

The Wikipedia page on mechanoreceptors: https://en.wikipedia.org/wiki/Mechanoreceptor says

"A mechanoreceptor is a sensory neuron that responds to mechanical pressure or distortion."

A specific example I know a lot about is a hair cell of the inner ear. The Wikipedia page for stereocilia has this description (https://en.wikipedia.org/wiki/Stereocilia_(inner_ear)):

"In the inner ear, stereocilia are the mechanosensing organelles of hair cells, which respond to fluid motion in numerous types of animals for various functions, including hearing and balance. They are about 10–50 micrometers in length and share some similar features of microvilli.[1] The hair cells turn the fluid pressure and other mechanical stimuli into electric stimuli via the many microvilli that make up stereocilia rods.[2] Stereocilia exist in the auditory and vestibular systems."

To add to that, each hair cell has a specialized cilium called a kinocilium that is surrounded by an array of actin-filiment based stereocilia. The entire array of actin filaments and the kinocilium are all required for transducing the signal of the fluid in the cochlea to a signal, so definitely not simply a TM receptor for hair cells, though it may turn out that one or more of those are involved in the process as well.

Anyway, let's please not make a term or definition that says that a mechanoreceptor is a TM protein until we find papers that indicate this is the way to go.

ValWood commented 4 years ago

I'm going to close this. It's not so important right now. I can keep this as "transmembrane signalling receptor"...it was just something I saw go by in a review and I thought it would be nice to capture the specificity, but it sounds not so simple. I will wait until I have EXP publications for this.

ValWood commented 2 years ago

I have a publication! Detection of surface forces by the cell-wall mechanosensor Wsc1 in yeast

Could I get mechanoreceptor activity Combining with a mechanical force and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.

parent transmembrane signaling receptor activity

reference PMID: 34666001 and PMID: 23907979

ValWood commented 2 years ago

Can this term be added? I guess I should have put it in a new ticket, but I thought it might be useful. to have this discussion to hand.

pgaudet commented 2 years ago

+[Term] +id: GO:0140897 +name: mechanoreceptor activity +namespace: molecular_function +def: "Combining with a mechanical force and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction." [PMID:23907979, PMID:34666001] +is_a: GO:0004888 ! transmembrane signaling receptor activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/18636 xsd:anyURI +created_by: pg +creation_date: 2022-07-22T14:23:45Z +