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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Missing parentage? rRNA N-glycosylase activity / toxin activity #21451

Open Antonialock opened 3 years ago

Antonialock commented 3 years ago

Hello,

should toxin activity be added as a parent to rRNA N-glycosylase activity ?

rRNA N-glycosylase activity has synonyms saporins, ricin, etc

ValWood commented 3 years ago

~But they are related synonyyms. Because it produces a toxin doesn't make this activity itself a toxin?~

Antonialock commented 3 years ago

Is this not always a toxic activity?

ValWood commented 3 years ago

It is a toxic activity, but not a toxin. A toxin is a harmful substance itself (like a poison), not something that is toxic.

ValWood commented 3 years ago

~So the term means that the molecule you are annotating actually acts as a toxin. Usually secreted pathogen molecules (Possibly always, but I am not sure about that).~

mah11 commented 3 years ago

But what does "acts as a toxin" mean? Getting into a cell and chopping up important bits seems like it ought to qualify.

More importantly/less flippantly, the text definition of GO:0090729 offers botulinum toxin and snake venom as examples, and:

"Botulinum neurotoxins (BoNTs) are proteases that cleave specific cellular proteins essential for neurotransmitter release." (PMID:16318699)

... and snake venoms contain dozens of different active compounds, many of which have enzymatic activities that contribute to venom effects.

I have always been a bit leery of the "toxin activity" term, but as long as it's there, and defined as it is, it looks like GO:0030598 could fit as a subclass -- as long as cleaving that particular bond in rRNA is bad for the cell where it's happening, and the situation fits the part_of GO:0035821 ! modulation of process of other organism part of the ontology-structure definition of toxin activity.

Antonialock commented 3 years ago

the rRNA N-glycosylase activity is secreted and disrupts host ribosomes by depurinating the rRNA

so just because the toxin has a toxic activity.... is doesnt mean that toxic activities exhibited by toxins are toxin activities?

head melt..

Antonialock commented 3 years ago

thanks midori.

I have always been a bit leery of the "toxin activity" term,

Yes I agree, but I presumed it is the sort of term that users might like as a grouping/search term so would be worthwhile to add until it is (or isn't) obsoleted

ValWood commented 3 years ago

Probably toxin should not exist. If you don't know the actual MF would just annotate to a BP

GO:0140418 effector-mediated modulation of host process by symbiont or similar... It does seem to be a grouping term for effectors of unknown function....

so yes, rRNA N-glycosylase activity does seem to fit under the existing toxin term as it only seems to occur happen as a "toxin"

Antonialock commented 3 years ago

GO:0140418 effector-mediated modulation of host process by symbiont or similar...

I annotated to modulation by symbiont of host translation

Antonialock commented 3 years ago

(it is an effector in the sense that it is secreted - but I co-annotated to "extracellular region"m I presume that is sufficient and that the BP doesn't need to mention the fact it is an effector? - I'm not sure? )

ValWood commented 3 years ago

modulation by symbiont of host translation

sounds like the correct term. This term will probably be renamed to "disruption by symbiont of host translation"

ValWood commented 3 years ago

@pgaudet we should discuss toxin further on the multispecies call. By this, all effectors would be 'toxin activity'....

pgaudet commented 3 years ago

Sure OK let's add this to the multi org call agenda Some references: https://en.wikipedia.org/wiki/Ribosome-inactivating_protein https://pubmed.ncbi.nlm.nih.gov/2930487/

Antonialock commented 3 years ago

for reference I was annotating a fungal protein "mucoricin" 33462434