intracellular defense response

[gocentral]

I am trying to add some terms to the NLR gene family. However I feel that there could be more specific terms for this class of proteins. See PMID: 15967716

GO:0009595 detection of biotic stimulus has no child terms that would be suitable for proteins which detect intracellular pathogen-associated molecular patterns.

Please could a child term be created along the lines of: GO:0009596: detection of pest, pathogen or parasite but which does not have the parent "detection of external stimulus".

Also GO:0006952 defense response also has no child terms that could be used for intracellular defense.

The ideal term would be GO:0042829 defense response to pathogen. But again this has external parents (I hope that makes sense)

Thanks

Ruth

Reported by: RLovering

Original Ticket: "geneontology/ontology-requests/3053":https://sourceforge.net/p/geneontology/ontology-requests/3053

[gocentral]

Logged In: YES user_id=865072

Ruth,

I appreciate your interest in this area of the ontology which is currently under active development. The DAG under response to stimulus has been discussed over the past year and most recently at the GO Content Meeting held November 15-16 of this year, and a series of changes to the GO have been discussed and accepted by interested parties. Included in these changes are elimination of term such as "defense response to pathogen" and "detection of pest, pathogen, and parasite" in favor of organism specific term such as "defense response to bacteria," which do not prejudge the outcome of infection. Plants and animals react to LPS regardless of whether its source is considered a pathogen or not. I would be happy to send you further discussion of this topic if you like.

We do have existing terms in the GO, such as GO:0008329 pattern recognition receptor activity, a molecular function term, which may be of use to you. Similarly, annotation to GO:0042742 defense response to bacteria may be appropriate as well as a process annotation. A further annotation to GO:0045087 innate immune response seems entirely warrented as well. The fact that these proteins are found intracellularly suggests that coannotation to GO:0005622 intracellular or one of its children would be sufficient to establish the localization of the defense response.

New process terms are currently planned for annotation of proteins involved in the processes of recognition of PAMPs. I will make sure that such terms include one or more applicable to NLRs.

Anyway, as I prepare the various modified response, defense response, immune response, and related DAGs for integration with the existing GO, I will consider the question of localization in regards to defense response. My sense is that such a term is not clearly needed, and might require the addition of a corresponding extercellular defense response term as well.

-- Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=614564

Ruth,

In the new defense response structure we plan on having terms such as 'response to xxx-associated molecules', where xxx could either be bacteria or fungus or oomycetes etc. These terms will be incorporated into GO soon(As Alex mentioned, there is an active discussion going on, on this topic). Alex can give you the time frame for adding some of these terms so that you will have a better idea when you can use them for your annotation.

Suparna

Original comment by: smundodi

[gocentral]

Logged In: YES user_id=451873

Hi Ruth - we're about to undertake a major revision of these terms which I'm presuming will resolve the problems you mention...I'll check with Alex...

Original comment by: jl242

[gocentral]

Logged In: YES user_id=865072

Ruth,

I'm closing this item now with the implementation of the immunology revision. I will point out below a number of new terms which may be appropriate for your use. There may be other terms as well. If there are still terms missing, I think it is better to open a new SF item to cover them.

Thanks,

Alex

New Terms:

[Term] id: GO:0002818 name: intracellular defense response namespace: biological_process def: "A physiological defense response which occurs intracellularly." [GOC: add] exact_synonym: "intracellular defence response" [] is_a: GO:0006968 ! cellular defense response

[Term] id: GO:0002224 name: toll-like receptor signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GOC:add, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID: 15585605, PMID:15728447] comment: Note that the vertebrate toll-like receptors, unlike the Drosophila Toll molecule, directly bind their ligands. The Drosophila Toll molecule requires the Sptzle factor to bind microbial ligands and then the receptor in order to initiate innate immune responses. exact_synonym: "TLR signaling pathway" [ISBN:0781735149] is_a: GO:0002221 ! pattern recognition receptor signaling pathway

[Term] id: GO:0002752 name: cell surface pattern recognition receptor signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of binding to a cell surface pattern recognition receptor (PRR). Such receptors bind for molecular patterns based on a repeating or polymeric structures, like those of polysaccharides or peptidoglycans, which are sometimes associated with potential pathogens." [GOC:add, ISBN:0781735149, PMID:15199967] exact_synonym: "cell surface PAMP receptor signaling pathway" [] exact_synonym: "cell surface pathogen receptor signaling pathway" [] exact_synonym: "cell surface PRR signaling pathway" [] is_a: GO:0002220 ! innate immune response activating cell surface receptor signaling pathway is_a: GO:0002221 ! pattern recognition receptor signaling pathway

[Term] id: GO:0002753 name: cytoplasmic pattern recognition receptor signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of binding to a cytoplasmic pattern recognition receptor (PRR). Such receptors bind for molecular patterns based on a repeating or polymeric structures, like those of polysaccharides or peptidoglycans, which are sometimes associated with potential pathogens." [GOC:add, ISBN:0781735149, PMID:15199967] exact_synonym: "cytoplasmic PAMP receptor signaling pathway" [] exact_synonym: "cytoplasmic pathogen receptor signaling pathway" [] exact_synonym: "cytoplasmic PRR signaling pathway" [] is_a: GO:0002221 ! pattern recognition receptor signaling pathway

[Term] id: GO:0002754 name: intracellular vesicle pattern recognition receptor signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of binding to a pattern recognition receptor (PRR) located within the membrane of an intracellular vesicle such as an endosome or lysosome. Such receptors bind for molecular patterns based on a repeating or polymeric structures, like those of polysaccharides or peptidoglycans, which are sometimes associated with potential pathogens." [GOC:add, ISBN:0781735149, PMID:15199967] exact_synonym: "intracellular vesicle PAMP receptor signaling pathway" [] exact_synonym: "intracellular vesicle pathogen receptor signaling pathway" [] exact_synonym: "intracellular vesicle PRR signaling pathway" [] is_a: GO:0002221 ! pattern recognition receptor signaling pathway

[Term] id: GO:0002755 name: MyD88-dependent toll-like receptor signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor and relying on the MyD88 adaptor molecule. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GOC:add, ISBN:0781735149, PMID: 12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID: 15728447] exact_synonym: "MyD88-dependent TLR signaling pathway" [] is_a: GO:0002224 ! toll-like receptor signaling pathway

[Term] id: GO:0002756 name: MyD88-independent toll-like receptor signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor not relying on the MyD88 adaptor molecule. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GOC:add, ISBN:0781735149, PMID: 12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID: 15728447] exact_synonym: "MyD88-independent TLR signaling pathway" [] is_a: GO:0002224 ! toll-like receptor signaling pathway

[Term] id: GO:0002237 name: response to bacterium associated molecule namespace: biological_process def: "A change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of bacterial associated molecules such as peptides derived from bacterial flagellin." [GOC:sm] exact_synonym: "response to bacteria associated molecule" [] exact_synonym: "response to bacterial associated molecule" [] is_a: GO:0009607 ! response to biotic stimulus relationship: part_of GO:0009617 ! response to bacterium

[Term] id: GO:0002238 name: response to fungus associated molecule namespace: biological_process def: "A change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of fungal associated molecules such as chito-octomer oligosaccharide." [GOC:sm] is_a: GO:0009607 ! response to biotic stimulus relationship: part_of GO:0009620 ! response to fungus

[Term] id: GO:0002240 name: response to oomycetes associated molecule namespace: biological_process def: "A change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of oomycete associated molecules." [GOC:sm] is_a: GO:0009607 ! response to biotic stimulus relationship: part_of GO:0002239 ! response to oomycetes

Original comment by: addiehl

[gocentral]

• status: open --> closed

Original comment by: addiehl

[gocentral]

• assigned_to: nobody --> aledie

Original comment by: mah11