Can we restore 'toxin activity' and related terms?

[Alexander Diehl]

Pascale and others,

First of all, discussion of this issue properly belongs on the 
pathogenesis at geneontology.org mailing list, and I would encourage 
that we move it there.

Secondly, I agree with Pascale that reinstatement of "toxin activity" 
probably makes sense because we continue to have terms like "cytokine 
activity," "hormone activity," and "chemoattractant activity" which 
refer to inherent properties or activities of particular gene 
products and provide useful ways to group them and to think about 
them, both in the general arena of biology, and in the GO.

Furthermore, I believe that suggesting GO:0050827 toxin receptor 
binding as a replacement for toxin activity in the original 
obsoletion was based on a poor analogy to other terms in the GO. 
Certainly, detoxifying certain toxins is a natural process in certain 
organism, and protein acting as an intentional receptor for a toxin 
where in doing so promotes the breakdown of the toxin is a true 
"toxin receptor."  However, the proteins usually used as receptors 
for toxin entry did not evolve for that function, are only being 
exploited for that purpose, and have other, true, functions which 
ought to be annotated in the GO.  Thus, I would favor obsoletion of 
GO:0050827 toxin receptor binding because it is an easily misapplied 
term, in addition to reinstatement of "toxin activity."

-- Alex


At 8:22 AM -0500 6/7/05, Pascale Gaudet wrote:
>Hello,
>
>There are a bunch of function terms related to 'toxin' that were 
>obsoleted because they were deemed to be grouping terms rather than 
>real functions. See SF 873136, 730669.
>
>I think the 'toxin activities' are analogous to 'chemoattractant 
>activities' and therefore should be restored. There is no other 
>function terms that can describe what these things do. For example, 
>amanitin inhibits RNA polymerase II and therefore DNA transcription, 
>resulting in arrest of protein synthesis and cell necrosis (PMID: 
>15657006). There is no function term to represent that.
>
>It is suggested that annotations to 'toxin activity' be replaced by 
>pathogenesis (a process) and 'toxin receptor binding'. I am not sure 
>all toxins have a receptor. Moreover, binding to that putative toxin 
>receptor would occur in another organism and is a 'disease' state, 
>therefore out of the realm of GO (isn't it?). Finally, these 
>suggested annotations do not capture the role of the toxin from the 
>point of view of the organism synthesizing it, which is to favor its 
>own survival by attacking another organism.
>
>I would like to know what others think about that.
>
>Pascale


-- 
Alexander Diehl, Ph.D.
Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131