allergene annotation

[Suparna Mundodi]

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