merge hypersenstive response with programmed cell death

[gocentral]

From the PAMGO jamboree...

The suggestion has come up that the term 'hypersenstive response' be merged into its current parent term 'programmed cell death'. This is because the thinking in the field is currently that the hypersenstive response is equivalent to programmed cell death in other species, so the distinction made in GO is artifical.

TAIR people need to look at this...

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/3457":https://sourceforge.net/p/geneontology/ontology-requests/3457

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I'll hand this over to our new curator, Donghui Li, when he starts on Monday, 7/24. His field of expertise is in plant pathology and plant-pathogen interaction so he's the appropriate one to comment on this. I'll help him set up an SF account, etc.

Original comment by: tberardini

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Hi,

My name is Donghui, I am a curator at TAIR. I am relatively new to GO, but have worked on hypersensitive response (HR) in plants as a postdoc.

My opinion is that we should keep the term hypersensitive response. Here is my thought:

There are several types of programmed cell death in plants:

Perhaps the most dramatic example of PCD in plants is that which occurs to form the water and nutrient conducting tubes that form the vascular system. Both xylem (the water-conducting cells) and phloem (the nutrient-conducting cells) undergo autolysis (cell death) as they differentiate and mature.

Another example of PCD in plants is senescence.

It is now generally accepted that hypersensitive response is also a type of PCD. However, HR differs from other types of plant PCD by the fact that during hypersensitive response, the cell death is in response to pathogen attack. So there is a distinction between HR and other types of PCD in plants and animals.

Original comment by: donghui

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I’m sending more comments in response to the SourceForge item #1524725: merge hypersenstive response with programmed cell death.

I have read the comments of Donghui (TAIR), and Marcus and Trudy (PAMGO -- http://wiki.geneontology.org/index.php/Talk:PAMGO\_work\_in\_p rogress#Hypersensitive_response), and also looked at some more papers. First, I want to say that I am trying to comment from the perspective of what I understand to be the guiding principles of PAMGO from the beginning---that we try to create terms that will be useful to annotate both prokaryotes and eukaryotes, pathogens as well as mutualists, and animals as well as plants. One of our ideas was that we hoped, through the use of GO, to be able to learn things we did not know before (in addition to creating knowledge through annotating the genes in our organisms). You all know the history of the desire for a term that we could use to annotate genes in our pathogens whose gene products were shown to play a role in inducing the endogenous process of PCD in plant cells during pathogen attack. I understand that there are two (at least) quite different types of PCD in both plants and animals---a PCD that is developmental (turned on by the plant or animal itself) and one caused by another organism (like a pathogen or a non-pathogenic symbiont, as described by Marcus). The important concept here seems to be that we need a term that differentiates those, but one that also captures an important process that occurs in both plant and animal cells under attack. I like Marcus’s proposal of a term “symbiont-induced programmed cell death” – this seems perfect for our needs, and it can be used by both animal and plant people. I personally would prefer that we make the term “hypersensitive response” a synonym to that term, so plant people can easily find the appropriate GO term, and also so that we have a broad term that will work for both plant and animal people. I think the Pseudomonas people would like to have a home where the secreted effectors of both the plant pathogenic pseudomonads and Yersinia, the animal pathogen, reside. It seems to me that most papers I have looked (e.g. PMID: 11755421) that talk about PCD induced by animal pathogens, like Salmonella, call it PCD because that is what it appears to be – a process that at the moment can be distinguished from development PCD only by what was the stimulus that started it (i.e. a pathogen in this case). If it becomes clear that the HR in plants is conceptually and biologically different from the PCD that is a normal part of development, like the formation of phloem cells, then at that time it seems that a distinguishing term, HR, is appropriate. For right now, it appears to me that that term would be confusing to the greater biological world as a whole, because the term “hypersensitive” means something quite different in the animal pathogen world. I would like to see GO terms developed that whenever possible speak to the unity across plants and animals (if possible, of course), rather than using terms that might artificially create a difference when there might be none, and which have very different meanings in the 2 worlds. So- --and sorry that is such a long-winded comment---that’s my concern about having a separate term – HR – for what seems to be symbiont-induced PCD, specifically in plants. Is that term necessary? Again, if the HR in plants is biologically different in important ways from the process of symbiont-induced PCD in animal cells, then it’s fine – so long as both terms – separate ones for plants and animals – have a common parent in the GO trees so we can use GO to find genes products we did not know existed, but that do similar things in 2 quite different hosts – plants and animals.

Also in line with the early guiding principles of PAMGO, and I think also of GO in general (re: Alex Diehl), I do not think the proposed term “programmed cell death induced by non-pathogen symbiont” is a good one, for the reason Marcus himself mentioned – that one cannot always tell when a microbe involved in an interaction with a host will turn out to be pathogenic or not – that was the main reason we went with the broad view of symbiosis from the beginning of the proposed PAMGO terms.

Original comment by: ccollmer

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Candace has raised a good point. One question, do you think if we can annotate bacterial effectors that trigger the HR to the new term 'symbiont-induced PCD'. If so, that would link plant and pathogen annotations together. On the other hand, the emphasis of the term HR does appear to be on the plant side and it may not be appropriate to annotate effector genes to the term HR. In this sense, the symbiont-induced PCD is better. What do you think?

Original comment by: donghui

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Dear Donghui and others:

Sorry it’s been so long since your last comment. You are absolutely correct in raising the question about whether we could annotate effectors to the proposed term “symbiont- induced PCD.” I’m sorry to have implied that in my last comment, as I forgot for a minute that these terms in this tree (under PCD) are meant to be for annotating genes in the host – the plant or the animal. So, GO terms appropriate for annotating bacterial effectors would have to be found under the “symbiosis” trees, where we have proposed a term that would be appropriate for annotating the effectors – those proteins produced by the microbe that travel into the plant or animal cell and then interact with the genes of the host – the plant or animal — involved in inducing PCD. I’m sorry to have confused the issue again, after we all worked so hard to fix it.

Candace

Original comment by: ccollmer

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assigning to Donghui based on Tanya's first comment

Original comment by: mah11

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• assigned_to: nobody --> donghui

Original comment by: mah11

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A consensus has been reached:

The term 'hypersensitive response' has been renamed 'plant-type hypersensitive response' to distinguish from the hypersensitive response in animals.

Additionally a new term 'host programmed cell death induced by symbiont' was created as suggested by PAMGO. plant-type hypersensitive response is_a host programmed cell death induced by symbiont

Also refer to the following link for full discussion

http://wiki.geneontology.org/index.php?title=PAMGO\_Hypersensitive\_Response&printable=yes

-Donghui

Original comment by: donghui

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• status: open --> closed-fixed

Original comment by: donghui