gocentral
commented
20 years ago Logged In: YES user_id=482748
Hi Alex,
I added a definition to GO:0008329 pattern recognition receptor activity last week when I was clearing out my SF entries. It reads:
definition: Combining with pathogen-associated molecular patterns to initiate a change in cell activity. Pathogen-associated molecular patterns are conserved molecular structures found in large groups of pathogens. definition_reference: PMID:14557290.
feel free to tweak it though! And I definately agree it should be moved from being a child of transmembrane receptor.
I seem to remember most of the 'receptor' terms were moved out from under the 'binding' node a while ago (eg pheromone receptor activity is not related to pheromone binding). Some relationships are still there though- the GO office should be able to tell you whether I'm remembering correctly or not. This would affect 'pattern recognition receptor activity' being a child of 'pattern binding' for example.
I like having the new specific binding terms- it would be good to expand on some of the definitions though to say what zymosan/lipopolysaccharide is for example. ISBN:0198506732 has some nice definitions for most of these compounds.
All the new X receptor terms you propose are fine by me and will be useful for insect curation.I don't know much about pattern recognition though other than from curation. Are the patterns always pathogen- associated? Becky
Original comment by: beckyfoulger
Pattern Recognition Terms
Pattern recognition of the structural motifs of potential pathogens leading to activation of innate immune responses is a prominent feature of both invertebrate and vertebrate immune systems. Definitive motifs for recognition and specific receptor activities should be recognized in the GO and below I define and refine existing terms as well as propose some new ones, as well as rearranging the DAG appropriately.
In this new scheme the new term "pattern binding" is a collection term for more specific terms describing the binding of various structural motifs of potential pathogens.
Similarly the term "pattern recognition receptor activity" serves as a collection term for more specific terms describing receptor activities for various structural motifs of potential pathogens. GO function purists may argue that these terms are superfluous, but I believe they may have use in situations where the exact motifs bound are unknown, as well as providing context for their child terms.
I am open to discussion of these items, and would welcome comments particularly by invertebrate focused curators.
-- Alex
The new DAG:
binding ; GO:0005488 --% pattern binding ; GO:NewTerm ----% polysaccharide binding ; GO:0030247 ------% zymosan biding ; GO:NewTerm --------% zymosan receptor activity ; GO:NewTerm ------% polysaccharide receptor activity ; GO:NewTerm --------% zymosan receptor activity ; GO:NewTerm ----% lipopolysaccharide binding ; GO:0001530 ------% lipopolysaccharide receptor activity ; GO:NewTerm ----% lipoarabinomannan binding ; GO:NewTerm ------% lipoarabinomannan receptor activity ; GO:NewTerm ----% peptidoglycan binding ; GO:0042834 ------% peptidoglycan receptor activity ; GO:0016019 ----% pattern recognition receptor activity ; GO:0008329 ------% polysaccharide receptor activity ; GO:NewTerm --------% zymosan receptor activity ; GO:NewTerm ------% lipopolysaccharide receptor activity ; GO:NewTerm ------% lipoarabinomannan receptor activity ; GO:NewTerm ------% peptidoglycan receptor activity ; GO:0016019
receptor activity ; GO:0004872 --% pattern recognition receptor activity ; GO:0008329 ----% polysaccharide receptor activity ; GO:NewTerm ------% zymosan receptor activity ; GO:NewTerm ----% lipopolysaccharide receptor activity ; GO:NewTerm ----% lipoarabinomannan receptor activity ; GO:NewTerm ----% peptidoglycan receptor activity ; GO:0016019 --% transmembrane receptor activity ; GO:0004888 ----% scavenger receptor activity ; GO:0005044
Terms:
1) GO:0008329 pattern recognition receptor activity
has no definition and is misplaced as a child of GO:0004888 transmembrane receptor activity, when in fact certain gene products involved in pattern recognition are found in intracellular locations.
Proposed Definition: Combining with an repeating or polymeric structure, such as a polysaccharide or peptidoglycan, to initiate a change in cell activity.
Revised parentage: is-a to GO:0004872 receptor activity, is-a to the new term "pattern recognition activity," below.
Proposed Comment: Note that this term and its child terms are intended for gene products which are directly coupled to a signal transduction pathway; gene products which recognize polymeric structures such as polysaccharides or peptidoglycans in extracellular space, but are not directly coupled to signal transduction pathway should use the term GO:000XXXX pattern binding or its chld terms instead.
2nd Proposed comment: Note that many gene products that are called "pattern recognition receptors" in the literature have a broad range of potential ligands and also can be annotated to GO:0005044 scavenger receptor activity as well.
References: PMID:12507420, PMID:12925128, PMID:14523544
2) GO:NewTerm pattern binding
Synonym: pattern recognition activity [~ synonym]
Definition: Interacting selectively with a repeating or polymeric structure, such as a polysaccharide or peptidoglycan.
Parentage: is-a to GO:0005488 binding.
Comment: Note that this term and its child terms are intended for annotation of gene products which function to recognize (bind) the repeating structural units such as polysaccharides or peptidoglycans commonly found in microbial cell walls and virions. If such binding is coupled to signal transduction, use GO:0008329 pattern recognition receptor activity instead.
References: PMID:12225919, PMID:12507420, PMID:12925128, PMID:14523544, PMID:12072369
[there may be some objection to the naming of this term, and certainly the term name and its synonym could be switched if necessary.]
3) GO:0030247 polysaccharide binding
Revised parentage: is-a to GO:0030246 carbohydrate binding, is-a to the new term "pattern binding," above.
4) GO:NewTerm polysaccharide receptor activity
Definition: Combining with a polysaccharide to initiate a change in cell activity.
Parentage: is-a to GO:0030247 polysaccharide binding, is-a to GO:0008329 pattern recognition receptor activity.
References: PMID:14707091
5) GO:NewTerm zymosan binding
Definition: Interacting selectively with zymosan.
Parentage: is-a to GO:0030247 polysaccharide binding.
References: PMID:14707091
6) GO:NewTerm zymosan receptor activity
Definition: Combining with zymosan to initiate a change in cell activity.
Parentage: is-a to the new term "polysaccharide receptor activity," above.
References: PMID:14707091
7) GO:0001530 lipopolysaccharide binding
New synonym: LPS binding [= exact synonym]
New synonym: endotoxin binding [< broad synonym]
Current definition: Interacting selectively with lipopolysaccharide (LPS, endotoxin in the outer membrane in Gram-negative bacteria) to membrane bound CD14 in monocytes and macrophages, as well as soluble CD14. Facilitated by a lipopolysaccharide binding protein.
Revised definition: Interacting selectively with lipopolysaccharide.
[The revised definition is more in conformance to GO standard definitions, grammatically correct, and does not add unnecessary specificity, when in fact the range of cellular receptors for LPS is still unclear.]
Revised parentage: is-a to the new term "pattern binding," above.
8) GO:NewTerm lipopolysaccharide receptor activity
Synonym: LPS receptor activity [= exact synonym]
Synonym: endotoxin receptor activity [< broad synonym]
Definition: Combining with lipopolysaccharide to initiate a change in cell activity.
Parentage: is-a to GO:0001530 lipopolysaccharide binding, is-a to GO:0008329 pattern recognition receptor activity.
References: PMID:14609719
9) GO:NewTerm lipoarabinomannan binding
Synonym: LAM binding.
Definition: Interacting selectively with lipoarabinomannan.
Parentage: is-a to the new term "pattern binding," above.
References: PMID:10586073
10) GO:NewTerm lipoarabinomannan receptor activity
Synonym: LAM receptor activity.
Definition: Combining with lipoarabinomannan to initiate a change in cell activity.
Parentage: is-a to the new term "lipoarabinomannan binding," above, is-a to GO:0008329 pattern recognition receptor activity.
References: PMID:10586073
11) GO:0042834 peptidoglycan binding
Revised parentage: is-a to the new term "pattern binding," above.
[The existing parentage of GO:0042834 peptidoglycan binding is not quite right: while peptidoglycan is often a component of bacterial cell wall, because it can be found in isolation, binding of peptidoglycan is not strictly a type of bacterial binding. Also, Harold and I agree that due to its peptide components peptidoglycan is not strictly a type of carbohydrate, just as LPS and LAM are not either due to their lipid components.]
Reference: PMID:14698226
12) GO:0016019 peptidoglycan recognition activity
I recommend the name of this term be changed to "peptidoglycan receptor activity," in order to conform to GO naming standards and avoid confusion with GO:0042834 peptidoglycan binding. The name change is justified also by the position of GO:0016019 in the DAG as a descendent of receptor activity. The existing name should be kept as a synonym (~ synonym).
I also propose that GO:0016019 be given the following definition , revised parentage, and comment.
Definition: Combining with a peptidoglycan to initiate a change in cell activity.
Revised parentage: is-a to GO:0042834 peptidoglycan binding, is-a to GO:0008329 pattern recognition receptor activity.
Comment: Note that only peptidoglycan recognition proteins with receptor activity should be annotated to this term; otherwise use GO:0042834 peptidoglycan binding instead.
Reference: PMID:14698226
13) GO:NewTerm response to yeast
Definition: 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 yeast.
Parentage: is-a to GO:0009607 response to biotic stimulus
References: PMID:14707091
14) GO:NewTerm detection of yeast
Definition: The series of events by which a stimulus from a yeast is received and converted into a molecular signal.
Parentage: is-a to GO:0009595 detection of biotic stimulus, part-of to the new term "response to yeast," above
Reference: PMID:14707091
15) GO:0005044 scavenger receptor activity
is undefined.
Proposed definition: Combining with acetylated low-density lipoproteins, advanced glycation end products, or other polyanionic ligands to initiate a change in cell activity.
Proposed comment: Note that many gene products that are call "scavenger receptors" have a broad range of potential ligands and also can be annotated to GO:0008329 pattern recognition receptor activity or its child terms, or to GO:0030228 lipoprotein receptor activity or its child terms, as well.
References: PMID:11790542, PMID:12379907, PMID:12621157
16) GO:0008019 macrophage receptor activity should be obsoleted.
This undefined term was probably created to annotate the gene product MARCO, which really has both pattern recognition receptor activity and scavenger receptor activity.
Calling something a macrophage receptor activity is ambiguous in any case, because the term name could either imply an activity of a gene product found on macrophages or an activity used to detect macrophages.
Comment for obsoletion: This term was obsoleted because its name is ambiguous, and it was never defined. Consider annotating to the terms GO:0005044 scavenger receptor activity or GO:0008329 pattern recognition receptor activity or its child terms instead.
Reported by: addiehl
Original Ticket: "geneontology/ontology-requests/1707":https://sourceforge.net/p/geneontology/ontology-requests/1707