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allergene annotation
Michelle Gwinn Giglio
mlgwinn at tigr.org
Wed Mar 15 12:02:48 PST 2006
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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>>>
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