Search Mailing List Archives
allergene annotation
Michelle Gwinn Giglio
mlgwinn at tigr.org
Wed Mar 15 11:48:46 PST 2006
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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>>>
>
>
More information about the go-discuss
mailing list