allergene annotation

[Alexander D. Diehl]

Michelle,

Great paper, although I don't think they actually identified a specific 
Botrytis cinerea gene that promotes the HR response in the host to which 
one could tie the "induction of hypersensitive response in other 
organism" annotation.  But maybe I skimmed too quickly or that's coming 
in the next paper.

-- Alex


Michelle Gwinn Giglio wrote:
>
>
> Hi Suparna,
>
> I'm not an expert on this either - I'm hoping Candace will chime in.
>
> In the meantime, according to my understanding of what was discussed 
> at the recent PAMGO workshop, some pathogens intentionally induce the 
> HR in plants.   Some of these are necrotrophic and require (or at 
> least can use) dead tissues for growth.   Check out the abstract for 
> this paper PMID:10898976 - it describes how the HR response allows 
> Botrytis cinerea to grow on plants.  In addition, some pathogens shift 
> from biotrophy (living on live tissue) to necrotrophy during an 
> infection (hemibiotrophs) and at least one gene has been found in P. 
> sojae which is expressed at this transition and is believed to induce 
> HR.  That's examples from two systems - I imagine there are more.
>
> But Candace should be the one to comment on this as she knows much 
> more about it.
>
> Michelle
>
>
>
>
> Alexander D. Diehl wrote:
>
>> Suparna,
>>
>> I don't know if this is true as I am not an expert here, but Michelle 
>> wrote "it appears that pathogens (or at least plant ones) have the 
>> ability to manipulate and effect MANY plant systems," and mentioned 
>> the hypersensitive response in her discussion, I thought she was 
>> implying that manipulating the hypersensitive response is in fact 
>> done by certain microbes for their benefit.
>>
>> -- Alex
>>
>>
>> Suparna Mundodi wrote:
>>
>>>
>>>
>>> Alexander D. Diehl wrote:
>>>
>>>> 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, 
>>>
>>>
>>> Alex,
>>>
>>> I am not sure if I have heard of a situation where plant 
>>> hypersensitive response benefitting a microbe. Is there such a thing?
>>>
>>> Suparna
>>>
>>>
>>>
>>> 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