allergene annotation

[Michelle Gwinn Giglio]

Hi Jane, Alex, and all,

It's funny this is coming up now since at the recent PAMGO workshop held 
here at TIGR, we needed to annotate a gene from a pathogen to the 
process of inducing hypersensitive response in a plant.

In fact we were planning on requesting just such a term as "induction of 
hypersensitive response in other organisms". 

However, we also then started into a discussion of whether this was the 
best annotation approach to deal with this kind of situation - as it 
appears that pathogens (or at least plant ones) have the ability to 
manipulate and effect MANY plant systems and we fear a duplication of 
much of the process tree under "interaction between organism" - so we 
were wondering if the dual-taxon thing could work for this too.

Anyway - my point here was really to say that, yes indeed, there are 
cases where organims have proteins which induce the hypersensitive 
response in orther organisms.

I forget why they do this (at least the ones we were looking at) - its 
not my field - but I think it has to do with feeding - but I'm not sure.

Michelle





Jane Lomax wrote:

>LOL!
>
>Okay, okay - I take your point - the hay-fever example wasn't entirely 
>serious. Although I do remain to be convinced that there are _no_ cases 
>where inducing a hypersensitive response in another organism doesn't 
>confer some selective advantage, but I don't know enough about this 
>field and will bow to your superior knowledge ;)
>
>Out of interest (and I remember having this discussion with you before 
>Alex, I just can't remember the conclusion) what's the rationale behind 
>having GO:0016068 (type I hypersensitivity) in the ontology if all 
>hypersensitivities are disregulations?
>
>thanks,
>
>jane
>
>
>
>On Tue, 14 Mar 2006, Alexander Diehl wrote:
>
>  
>
>>No,
>>
>>Allergen and antigens are simply the substrates of the immune system.  
>>What makes something an allergen or an antigen is  dependent on the 
>>responding immune system, and varies by both individual and species.  A 
>>response to a particular allergen or antigen is a phenotypic quality of 
>>the responding organism.  Furthermore, allergies are far more prevalent 
>>in "western" human populations than in societies with less 
>>well-developed systems of sanitation and medicine, and thus reflect 
>>largely an inappropriate refocusing of the immune system in the absence 
>>of the threats humans faced in evolution, primarily parasites.  The 
>>suggestion that an allergen confers an advantage to plant reproduction 
>>also seems amazingly far fetched, given that the vast majority of plant 
>>pollen ends up somewhere else than up a person's nose.  Even in sneezing 
>>(if I am to pursue what may be intended facetiously here), the pollen 
>>would be primarily expelled covered in mucus and probably inactivated.
>>
>>Allergies are pathogenic disregulations of the normal "hypersensitivity" 
>>responses.  We should not be stretching the GO to become a disease 
>>ontology unless that is what we want to do with it.  If we want to make 
>>the GO into a disease ontology then let's do it officially and not on 
>>the sly.
>>
>>-- Alex
>>
>>
>>Jane Lomax wrote:
>>    
>>
>>>I concede that the argument doesn't hold up as well for allergens as it 
>>>does for pathogenic organisms.
>>>
>>>But aren't you making a value judgement about what constitutes a 'normal' 
>>>interaction? How do we know that the fact that the plant protein induces a 
>>>hypersensitive response in another organism doesn't confer some advantage 
>>>to the plant? Perhaps hay-fever promotes the spreading of pollen?!
>>>
>>>jane
>>>
>>>
>>>On Tue, 14 Mar 2006, Alexander Diehl wrote:
>>>
>>>  
>>>      
>>>
>>>>Sorry to be a few minutes late on this.
>>>>
>>>>The function of a protein, any protein, is not to be an allergen, or 
>>>>antigen, for another organism's immune system.  This is not appropriate 
>>>>annotation at all.  Indeed, nearly any protein can be made antigenic 
>>>>when given in the right context.  The plant proteins in question may be 
>>>>known allergens, but that is not their natural role in the plant or for 
>>>>the plant.  Annotation of allergenic potential would be appropriate with 
>>>>an ontology focused on disease and pathology, but not for the GO.
>>>>
>>>>We can discuss at the meeting, but I am quite firm in my conviction here,
>>>>
>>>>Alex
>>>>
>>>>
>>>>Jane Lomax wrote:
>>>>    
>>>>        
>>>>
>>>>>But I think when you're talking about interactions between organisms, 
>>>>>there really isn't a 'normal' or 'abnormal' - the interaction just 
>>>>>occurs. And remember that you'll record two taxon ids; one for the species 
>>>>>producing the allergen, and one for the 'allergic' species. So it isn't 
>>>>>the usual case of 'is it normal for the species I'm annotating' because 
>>>>>you're annotating both.
>>>>>
>>>>>jane
>>>>>
>>>>>On Tue, 14 Mar 2006, Harold Drabkin wrote:
>>>>>
>>>>>  
>>>>>      
>>>>>          
>>>>>
>>>>>>Yes, a new term would work much better.  However, it may or may not be 
>>>>>>the "normal " function or process.
>>>>>>A virus or symbiont host interaction is a bit different, because those 
>>>>>>interactions are most likely critical for the life cycle (eg, if you 
>>>>>>don't have a host, the virus can't replicate, etc.).  Many people are 
>>>>>>allergic to gluten, but is that a normal function/process of  gluten? 
>>>>>>
>>>>>>
>>>>>>Jane Lomax wrote:
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>>
>>>>>>>Unfortunately that term only works where one organism is living in 
>>>>>>>symbiosis with another organism (e.g. host/pathogen) which is why I 
>>>>>>>suggested that new term...
>>>>>>>
>>>>>>>
>>>>>>>On Tue, 14 Mar 2006, Harold Drabkin wrote:
>>>>>>>
>>>>>>>  
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>>>
>>>>>>>>But, I did find this term, and related?
>>>>>>>>
>>>>>>>>GO term: 	*induction of host defense response*
>>>>>>>>GO id: 	*GO:0044416*
>>>>>>>>Definition: 	*The elicitation by an organism of the defense response of 
>>>>>>>>the host. The host is defined as the larger of the organisms involved in 
>>>>>>>>a symbiotic interaction. *
>>>>>>>>
>>>>>>>>
>>>>>>>>which I think might be more in line with a direct annotation to 
>>>>>>>>something like this???
>>>>>>>>
>>>>>>>>
>>>>>>>>Harold Drabkin wrote:
>>>>>>>>    
>>>>>>>>        
>>>>>>>>            
>>>>>>>>                
>>>>>>>>
>>>>>>>>>I would not; they are the a cause, but they are not involved in the 
>>>>>>>>>process (which is not occurring in the plant).
>>>>>>>>>The GO is used to indicate the normal function and process of a gene 
>>>>>>>>>product. You need to look at it from the point of view of the organism 
>>>>>>>>>that produces the gene product. If these perform some function for the 
>>>>>>>>>plant, that is what you would annotate them to. Perhaps there are 
>>>>>>>>>terms associated with defense in a plant (ie, along the lines of 
>>>>>>>>>something that is released to deter the plant from being eaten???__?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>adepto at cribi.unipd.it wrote:
>>>>>>>>>      
>>>>>>>>>          
>>>>>>>>>              
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>>>Hi All
>>>>>>>>>>I have to annotate plant genes described as "allergenic peptides" in 
>>>>>>>>>>pFam these
>>>>>>>>>>genes are described as:
>>>>>>>>>>"Allergies are hypersensitivity reactions of the immune system to 
>>>>>>>>>>specific
>>>>>>>>>>substances called allergens (such as pollen, stings, drugs, or food) 
>>>>>>>>>>that, in
>>>>>>>>>>most people, result in no symptoms. A nomenclature system has been 
>>>>>>>>>>established
>>>>>>>>>>for antigens (allergens) that cause IgE-mediated atopic allergies in 
>>>>>>>>>>humans..."
>>>>>>>>>>
>>>>>>>>>>So, where may I annotate these allergenes? It is GO:0016068 (type I
>>>>>>>>>>hypersensitivity) the right term? Thanks in advance.
>>>>>>>>>>Alessandro
>>>>>>>>>>  
>>>>>>>>>>        
>>>>>>>>>>            
>>>>>>>>>>                
>>>>>>>>>>                    
>>>>>>>>>>
>>>>>>>>    
>>>>>>>>        
>>>>>>>>            
>>>>>>>>                
>>>>>>>>
>>>>>>>Dr Jane Lomax
>>>>>>>GO Editorial Office
>>>>>>>EMBL-EBI
>>>>>>>Wellcome Trust Genome Campus
>>>>>>>Hinxton
>>>>>>>Cambridgeshire, UK
>>>>>>>CB10 1SD
>>>>>>>
>>>>>>>p: +44 1223 492516
>>>>>>>f: +44 1223 494468
>>>>>>>
>>>>>>>  
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>>>
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>>
>>>>>Dr Jane Lomax
>>>>>GO Editorial Office
>>>>>EMBL-EBI
>>>>>Wellcome Trust Genome Campus
>>>>>Hinxton
>>>>>Cambridgeshire, UK
>>>>>CB10 1SD
>>>>>
>>>>>p: +44 1223 492516
>>>>>f: +44 1223 494468
>>>>>
>>>>>  
>>>>>      
>>>>>          
>>>>>
>>>>-- 
>>>>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 
>>>>
>>>>
>>>>    
>>>>        
>>>>
>>>Dr Jane Lomax
>>>GO Editorial Office
>>>EMBL-EBI
>>>Wellcome Trust Genome Campus
>>>Hinxton
>>>Cambridgeshire, UK
>>>CB10 1SD
>>>
>>>p: +44 1223 492516
>>>f: +44 1223 494468
>>>
>>>  
>>>      
>>>
>>-- 
>>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 
>>
>>
>>    
>>
>
>Dr Jane Lomax
>GO Editorial Office
>EMBL-EBI
>Wellcome Trust Genome Campus
>Hinxton
>Cambridgeshire, UK
>CB10 1SD
>
>p: +44 1223 492516
>f: +44 1223 494468
>
>  
>