allergene annotation

[Michelle Gwinn Giglio]

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