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allergene annotation

Michelle Gwinn Giglio mlgwinn at tigr.org
Wed Mar 15 11:24:45 PST 2006



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
>>>>>
>>>>>  
>>>>>
>>>
>>>
>
>



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