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allergene annotation

Alexander D. Diehl adiehl at informatics.jax.org
Wed Mar 15 09:50:06 PST 2006


Michelle,

I think it's very important to distinguish between microbial products 
that enable a microbe to manipulate its environment within a host 
organism in a way that benefits the microbe, and products that are 
simply responded to because of the inherent ability of the host to 
recognize specific molecular patterns evolutionarily associated with the 
presence and potential danger of a microbe and mount a response intended 
to protect the host.  The first type is a valid microbial process of 
inducing a response in another organism, whereas as the second process 
is strictly a host process acting upon a substrate in the environment.  
The second situation corresponds to the recognition of 
antigens/allergens by a vertebrate immune system.  The only process 
involved is a host process.

Clearly in the case of induction of the plant hypersensitive response by 
microbes, if that induction benefits the microbe in some way, it is a 
valid process for the microbe, otherwise it is simply a host defense 
response.  We need to maintain the distinction here in how we annotate 
to the GO, and in some situations the existing experimental evidence may 
not support an annotation to a microbial process.

-- Alex


Michelle Gwinn Giglio wrote:
>
>
>
> 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
>>
>>  
>>


-- 
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




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