def of 'symbiotic process' GO:0044403

[mgiglio99]

Per our discussion at GOC meeting - broaden definition of 'symbiotic process' GO:0044403 so that it includes both gene products from symbiont and host. Current def specifies symbiont.

Here is a suggestion - Change first sentence FROM old sentence: "A process carried out by symbiont gene products that enables the interaction between two organisms living together in more or less intimate association." TO new sentence: "A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism."

@ValWood @pgaudet @nsuvarnaiari @pmasson55 What do you think?

[addiehl]

With this suggested change, all processes necessarily belong to one organism only, such that no process that depends on gene products from both organisms would be covered, and all processes carried out by an organism's gene products act only within that organism alone, and not within the symbiont or externally.

I find this is too limiting. Alex

[ValWood]

~So this term needs to be more specific about the types of process? The gene products annotated may be from pathogen or host, but they should only be the gene products that are specifically involved in pathogen host interactions. Is this what you are saying, if so I agree :) i.e even housekeeping genes in the symbiont enable the symbiosis, but here we mena the gene products at the pathogen host interacgtion interface. Here I get stuck because ont he problem I work on the pathogen host interaction is defined "Any of the set of observable disease formation characteristics arising from the interaction of a potentially pathogenic organism with a host organism" i.e it is the processes related to pathology. But we need to define them without reference to the disease causing phenotypes. Tricky!~

I was barking up the wrong tree

[addiehl]

The formation of 'actin rockets' by listeria resident in host cells is an example of a symbiotic process that relies on gene products of both the symbiont and the host. The process itself takes place externally to the listeria cells but internally to the host cells. https://www.mechanobio.info/pathogenesis/what-are-actin-comet-tails/

So this process by its nature is not a symbiotic process according to the new definition of symbiotic process, because it relies on gene products of both symbiont and host and takes place outside the symbiont. However, I believe it is a symbiotic process according to any normal understand of symbiosis.

[mgiglio99]

Hi Alex, I was going for what you said, but I didn't phrase it correctly. Was trying to keep to the structure of what the previous def had. Let's work on alternatives.

[mgiglio99]

@addiehl How about this for the first sentence:

"A process carried out by gene products from one or more organisms that enable the organism(s) to engage in a symbiotic relationship, a more or less intimate association, with another organism."

[pgaudet]

See also #15497

[ValWood]

Do we have a written explanation anywhere of why we always use "symbiont" in preference to "pathogen". The group I am working with objected to 'symbiont'; on the grounds that they are working with obligate pathogens (necrotrophic fungi). I tried to explain the rationale but I was getting on OK until the 'necrotrophs' where there is no symbiosis, the feed on dead plant matter. Could you point me to any text describing the rationale that I can use to explain to them? I'm sure that it exists somewhere.

[pgaudet]

Because not all symbionts are pathogens, and even pathogens are not always pathogenic, it may depend on the life stage. SO symbiont must stay as the term label.

I can add synonyms if needed.

Thanks, Pascale

[ValWood]

I understand that symbiont must stay as the label. I think synonyms will be useful.

I just wondered if there was a formal explanation anywhere (I toid them this!). I also ecxplained that it would not make sense to replicate everything as "symbiotic" and "pathogenic" But I see their point for the necrotrophs. they evolved to kill the host. They are never symbionts. For other pathogens their 'purpose' isn't to kill the host, they require the host to survive.

[mgiglio99]

The thing is that I'm sure that those necrotrophs are not able to kill all species so for the species they don't kill they are not pathogens. (It sounds like for such species they don't have any interactions at all so they would not be any kind of symbiont for those species.) And I think we should avoid saying things about "purpose" - non of these species evolved with a goal in mind - I know you know that and I'm sure they know that - but I do think it's important to be careful about the language used which can lead to thinking about this stuff in ways that can mislead. These organisms didn't evolve to kill their hosts, they survived and expanded when one of them evolved the ability to kill tissue and use it as a food source. It just so happens that can result in the death of the host. And it's important to remember that symbiosis encompasses all types of intimate interactions whether beneficial or harmful. So being an obligate pathogen is still a symbiosis. Text on this stuff appears in the PAMGO papers. I'll have to chase down the one that would be best.

[ValWood]

I think this is the most useful thing"symbiosis encompasses all types of intimate interactions whether beneficial or harmful" because this was the part I was having . trouble convincing, so I was beginning to doubt it. So the necrotrophs are fine too.

The PAMGO citation would be useful.