allergene annotation

[Michelle Gwinn Giglio]

Hi Suparna,

Sure - it's PMID:12410814.
However, these may not be the best examples, in fact I'm sure they are 
not, I know very little about this, only what I've learned from PAMGO 
folks over relatively brief discussions of papers they were annotating.

Michelle



Suparna Mundodi wrote:

> Michelle,
>
> Do you have the P.sojae reference by any chance?
>
> Suparna
>
> Michelle Gwinn Giglio wrote:
>
>>
>>
>>
>> Hi Alex,
>>
>> Yeah - I'm not sure there was a specific gene for the Botrytis 
>> cinerea case yet identified - but it shows a system exists even if 
>> they haven't found the exact genes.  However, they have found such 
>> candidate genes in the P. sojae system.
>>
>> Michelle
>>
>>
>> Alexander D. Diehl wrote:
>>
>>> 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
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>>>