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Source ontology files for the Gene Ontology
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NTR: appressorium-mediated entry into host #21505

Closed Achchuthan closed 3 years ago

Achchuthan commented 3 years ago

Hi,

Can I request the following new term please?

Accession: GO:xxxxxx Name: appressorium-mediated entry into host Ontology: biological_process Synonyms: appressorium-mediated host invasion, appressorium-mediated host penetration, appressorium-mediated invasion into host, appressorium-mediated penetration into host Definition: Penetration by a symbiont into a host organism via appressorium. The host is defined as the larger of the organisms involved in a symbiotic interaction. is_a: GO:0044409 ! entry into host Source: PMID:14731267, PMID:22589729, GOC:ach

Thanks & best wishes, Achchuthan

ValWood commented 3 years ago

Hi AGO:0075016 JSON appressorium formation Biological Process

Definition (GO:0075016 GONUTS page) The process in which a swollen, flattened portion of a symbiont filament is formed on or near its host organism, to adhere to and for the purpose of penetrating the host surface.GO:0075016 JSON appressorium formation Biological Process

Definition (GO:0075016 GONUTS page) The process in which a swollen, flattened portion of a symbiont filament is formed on or near its host organism, to adhere to and for the purpose of penetrating the host surface.ch,

this term already exists: (it is under GO:0075015 formation of infection structure, a child of entry into host)

GO:0075016 appressorium formation The process in which a swollen, flattened portion of a symbiont filament is formed on or near its host organism, to adhere to and for the purpose of penetrating the host surface.

pgaudet commented 3 years ago

We also have "GO:0075001 adhesion of symbiont appressorium to host".

Based on https://en.wikipedia.org/wiki/Appressorium, it looks like appressorium formation, adhesion to host and penetration are coupled processes, or even substeps of the same process. Should we consider having a single term that describes the entire process?

Thanks, Pascale

ValWood commented 3 years ago

I think a single process would do . I 'm not sure that we know the individual molecular steps.

ValWood commented 3 years ago

The appressorium forms a penetration peg, and we also have this unused term under GO:0075015 formation of infection structure GO:0075053 penetration peg formation This term is not used.... Which species form penetration pegs? Is this fungal specific? @mgiglio99

krchristie commented 3 years ago

We have quite a number of appresorium terms:

and also three other terms that mention "appressorium" in their definition:

Achchuthan commented 3 years ago

I think we need a separate term for appressorium formation (GO:0075016). As described in PMID:22589729, some of the mutants do not affect appressorium formation, but results in defective appressorium mediated penetration. But, I think GO:0075001 (adhesion of symbiont appressorium to host) could be combined with this requested term (appressorium-mediated entry into host). Otherwise, I am wondering whether it would be possible to keep all these as separate terms and create an overall parent term to cover all these terms, if this makes sense?

Thanks, Achchuthan

krchristie commented 3 years ago

Hi @Achchuthan

Unfortunately, it is quite hard to see the part_of relationships, but looking through the relationships, the term "appressorium formation" is already meant to be the general term. It has these EXACT synonyms:

and is_a: GO:0075015 ! formation of infection structure

Here are the relationships I see between the non-regulation terms, where I am using dashes to indicate nesting of terms:

-- GO:0075016 - appressorium formation

--- GO:0075035 - appressorium maturation [part_of 'appressorium formation'] ---- GO:0075039 - establishment of turgor in appressorium [part_of 'appresorium maturation'] ---- GO:0075043 - melanization of appressorium wall [SubClassOf 'appresorium maturation'] ?? _should this be part_of instead of isa ??

--- GO:0075033 - appressorium septum formation [part_of 'appressorium formation']

--- GO:0075025 - initiation of appressorium formation [part_of 'appressorium formation'] ---- GO:0075029 - formation of appressorium germ tube hook structure [part_of 'initiation of appressorium formation]

--- GO:0075034 - nuclear division involved in appressorium formation [part_of 'appressorium formation']

Then this term does not seem to be placed in the part_of relationship structure with any of the other appressorium terms. Where should this term be placed in relationship to the rest of the terms?

ValWood commented 3 years ago

There are way too many terms here, that were added with no use case or reference.

we should definitely obsolete GO:0075033 - appressorium septum formation GO:0075034 - nuclear division involved in appressorium formation (unused)

These are just describing the division resulting in the specialized cell type. They are too specific.

ValWood commented 3 years ago

But, I think GO:0075001 (adhesion of symbiont appressorium to host) could be combined with this requested term (appressorium-mediated entry into host).

Note that this is a term pending obsoletion because it represents a MF in the BP ontology.

ValWood commented 3 years ago

Note that the multi-organism group are aware of problems in the penetration of host branch,as part of the multi-species branch revisions: https://github.com/geneontology/go-ontology/issues/18465#issuecomment-567712520 but we haven't got to it yet.

Achchuthan commented 3 years ago

Hi @krchristie,

Thank you very much for laying out the relationships between these terms.

Thanks, Achchuthan

Achchuthan commented 3 years ago

There are way too many terms here, that were added with no use case or reference.

we should definitely obsolete GO:0075033 - appressorium septum formation GO:0075034 - nuclear division involved in appressorium formation (unused)

These are just describing the division resulting in the specialized cell type. They are too specific.

I agree. I will never be using these terms in my annotations.

krchristie commented 3 years ago
  • As of now, I think "GO:0075003 - adhesion of symbiont appressorium to host" can only be placed in this relationship: is_a "adhesion of symbiont infection structure to host". This is already added to the GO term.

Actually, I think "GO:0075003 - adhesion of symbiont appressorium to host" could stay as is_a "adhesion of symbiont infection structure to host" and also be part_of "appressorium formation", which seems like it should be since it is defined as what keeps the appressorium attached to the host, so it seems like it should have some relationship to "appressorium formation".

Here is our current definition of this term:

"GO:0075003 - adhesion of symbiont appressorium to host" Def: The attachment of an appressorium of the symbiont to its host via adhesion molecules. The host is defined as the larger of the organisms involved in a symbiotic interaction.

  • I am wondering whether we should leave "GO:0075003 - adhesion of symbiont appressorium to host" as it is or whether we should broaden the GO term/ definition/ synonyms for "Appressorium formation" (GO:0075016) to include adhesion and penetration. If we do so, "appressorium formation" will no longer be a is_a "formation of infection structure".

My knowledge of fungal infection structures is quite old from a really interesting fungal genetics meeting at least a decade ago. I took a quick look at Wikipedia: https://en.wikipedia.org/wiki/Appressorium and here are some select quotes from the Appressorium page:

Following spore attachment and germination on the host surface, the emerging germ tube perceives physical cues such as surface hardness and hydrophobicity, as well as chemical signals including wax monomers that trigger appressorium formation.

Appressorium formation begins when the tip of the germ tube ceases polar growth, hooks, and begins to swell.

Formation The attachment of a fungal spore on the surface of the host plant is the first critical step of infection. Once the spore is hydrated, an adhesive mucilage is released from its tip.[3] During germination, mucilaginous substances continue to be extruded at the tips of the germ tube, which are essential for germ tube attachment and appressorium formation.[4]

I am wondering what is supposed to be part of "appressorium formation", abd whether are steps that are part of infection that occur before or after "appressorium formation".

* I agree that GO:0075043 - melanization of appressorium wall should be 'part_of' instead of 'is_a'.

great.

Achchuthan commented 3 years ago
  • As of now, I think "GO:0075003 - adhesion of symbiont appressorium to host" can only be placed in this relationship: is_a "adhesion of symbiont infection structure to host". This is already added to the GO term.

Actually, I think "GO:0075003 - adhesion of symbiont appressorium to host" could stay as is_a "adhesion of symbiont infection structure to host" and also be part_of "appressorium formation", which seems like it should be since it is defined as what keeps the appressorium attached to the host, so it seems like it should have some relationship to "appressorium formation".

Sounds good to me!

Here is our current definition of this term:

"GO:0075003 - adhesion of symbiont appressorium to host" Def: The attachment of an appressorium of the symbiont to its host via adhesion molecules. The host is defined as the larger of the organisms involved in a symbiotic interaction.

  • I am wondering whether we should leave "GO:0075003 - adhesion of symbiont appressorium to host" as it is or whether we should broaden the GO term/ definition/ synonyms for "Appressorium formation" (GO:0075016) to include adhesion and penetration. If we do so, "appressorium formation" will no longer be a is_a "formation of infection structure".

My knowledge of fungal infection structures is quite old from a really interesting fungal genetics meeting at least a decade ago. I took a quick look at Wikipedia: https://en.wikipedia.org/wiki/Appressorium and here are some select quotes from the Appressorium page:

Following spore attachment and germination on the host surface, the emerging germ tube perceives physical cues such as surface hardness and hydrophobicity, as well as chemical signals including wax monomers that trigger appressorium formation.

Appressorium formation begins when the tip of the germ tube ceases polar growth, hooks, and begins to swell.

Formation The attachment of a fungal spore on the surface of the host plant is the first critical step of infection. Once the spore is hydrated, an adhesive mucilage is released from its tip.[3] During germination, mucilaginous substances continue to be extruded at the tips of the germ tube, which are essential for germ tube attachment and appressorium formation.[4]

I am wondering what is supposed to be part of "appressorium formation", abd whether are steps that are part of infection that occur before or after "appressorium formation".

It looks to me that "appressorium formation" is part of the infection process and infection process definitely starts before the formation of appressorium and continues during and after appressorium formation. I think that the infection process starts when the spores are attached to the host surface. The attachment of spore and germination precedes appressorium formation. As the appressorium matures, it becomes firmly attached to the host. So, you are right that "adhesion of symbiont appressorium to host" (GO:0075003) is part_of "appressorium formation". The infection process continues after appressorium formation with penetration of appressorium into the host. I'm not sure whether I have answered your question.

Achchuthan commented 3 years ago

Hi @krchristie, @ValWood, @pgaudet

A gentle reminder about this issue? Do we have any further developments regarding merging of appressorium-related terms and incorporating penetration into the new merged term?

Thanks, Achchuthan

krchristie commented 3 years ago

Hi @krchristie, @ValWood, @pgaudet

A gentle reminder about this issue? Do we have any further developments regarding merging of appressorium-related terms and incorporating penetration into the new merged term?

Thanks, Achchuthan

Hi @Achchuthan - Thanks for the reminder. I'm doing ontology work this week, so I'll put this on my priority list to work on again. Today, I'll go through the ticket and figure out what has been decided and what questions remain.

Thanks,

-Karen

Achchuthan commented 3 years ago

Hi @krchristie, Sounds good! Thanks!! Best wishes, Achchuthan

krchristie commented 3 years ago

This is what I see that we've agreed to do:

I've done the first 4 items, and will send out obsoletion emails tomorrow.

Let me know if you see anything I missed.

Achchuthan commented 3 years ago

Hi @krchristie. All of these sounds great! I don't think you have missed anything from the above discussion. Thanks a lot for taking your time to work on these changes. BW, Achchuthan

krchristie commented 3 years ago

Hi @krchristie. All of these sounds great! I don't think you have missed anything from the above discussion. Thanks a lot for taking your time to work on these changes. BW, Achchuthan

Hi @Achchuthan - sorry it took so long to get back to this. The discussion got complicated enough that it ceased to be a quick ticket to go through and figure out all the parts to be done.

I've opened a new ticket for the obsoletions: Proposal to obsolete two overly specific appressorium formation terms #21923

Since everything else we agreed on in this ticket, I'm going to close this ticket.

Thanks,

-Karen

Achchuthan commented 3 years ago

Hi @krchristie, I completely understand! This was not a straightforward issue and had several action items. Even, this issue slipped out of mind for some time. Thanks & best wishes, Achchuthan