Candace's email 21 July 2009

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Jane’s 3) Let me see if I can explain what I was thinking here in terms of our needing two different types of terms, and then everyone can comment on how I was getting off track.. I was thinking that the process of viral replication is similar to the hypersensitive response, a type of programmed death (PCD) in a plant cell, which we dealt with in PAMGO and realized that we needed two different types of terms (and added comments to each of these to help annotators use them correctly). In each case the process is basically the same, but in one case it is turned on by the plant itself, and in another it is induced (triggered, up-regulated) via a gene product produced by a symbiont (which triggers the plant cell to commit suicide by turning on its PCD pathway). These are the 2 GO terms, their definitions, and the comments for each:

a) GO:0009626 : plant-type hypersensitive response – Definition: The rapid, localized death of plant cells in response to invasion by a pathogen. COMMENT: Note that term is to be used to annotate gene products in the plant. To annotate symbiont gene products that induce the hypersensitive response, consider the biological process term 'modulation by symbiont of host defense-related programmed cell death ; GO:0034053'.

b) GO:0034053 : modulation by symbiont of host defense-related programmed cell death. Definition: Any process by which an organism modulates the frequency, rate or extent of defense-related programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. COMMENT: Note that this term is used to annotate gene products of the symbiont. To annotate host gene products, consider the biological process term 'plant-type hypersensitive response ; GO:0009626'.

So, in a corresponding way, it seemed that we would also need 2 terms here. One term – possibly “replication of virus within host cell” -- would be used for annotating viral gene products that are involved in the replication of the virus. Perhaps the second term (to be used for annotating plant gene products that get co-opted by the virus to help replicate the virus) would be something like “replication of viral symbiont by host.” Or, is everyone saying that it would be fine to annotate both viral genes and plant genes to the same parent term, “replication of virus within host cell”? Is this a different situation (from plant PCD) because the virus is actually doing all this within the plant cell (where it is not currently a separate “organism”? I’m a little confused about the important distinctions between these two situations (plant-type PCD versus viral replication). Can someone help here?