gocentral
commented
17 years ago Logged In: YES user_id=436423 Originator: YES
replies (also emailed) ...
> GO:0008907 integrase activity
I agree -- this definition is much too specific. I'll try to rephrase it so it doesn't restrict itself to lambdoid phage DNA.
> GO:0008979 prophage integrase activity
This term is also only used for 5 annotations, which could be transferred to the parent term (once the latter's definition has been sorted out). An alternative to making GO:0008979 obsolete may be to merge it into its parent, which has the advantage that it can be done immediately (we give a 2-week notice period for obsoletes). Do you have a preference?
> GO:0009037 tyrosine-based site-specific recombinase activity > > My comment: this defitnition is almost correct but should be > seen in the context of a parent term such as "DNA breakage > reunion activity". I presently have children for the term, to > cover recombination leading to integration, excision or > resolution. However a better solution may be to associate this > activity with the processes integration, excision or resolution?
Could you suggest a definition for a new term for "DNA breakage reunion activity"?
At present, we do not have any relationships between terms from different ontologies, so we cannot yet capture any connections between recombinase terms and the process terms for integration, excision, etc. As Jane may have told you, we are planning to add links between biological process and molecular function (once some tools are in place, and we've established what the relationship type will be), and your knowledge of the bacterial processes and the enzymes involved will be very helpful when we're ready to add the links.
> GO:0004803 transposase activity
Protein family membership per se is not used as a criterion for creating GO terms or determining their parentage, but because the DDE motif is involved in catalysis, we can phrase a definition that uses the DDE information.
> GO:0045090 retroviral genome replication
I agree, this definition needs considerable improvement -- in addition to the problem you've noticed, it also doesn't say what the beginning and end are.
The definition of the parent, 'viral genome replication', is also not ideal. I'll make some specific suggestions here.
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Original comment by: mah11
from an email to the GO list from Ariane Toussaint:
Accession GO:0008907 integrase activity Ontology molecular function Synonyms None Definition Catalysis of the integration of lambdoid phage DNA during establishment, probably by forming a transient DNA-protein link. [source: ISBN:0198506732] My comment This type of integration concerns far more genetic entities than lambdoid phage genomes. See my definition phi:0000132. Site-specific DNA integration: The process by which a segment of DNA is incorporated into another by a site-specific recombination event.
Accession GO:0008979 prophage integrase activity Ontology molecular function Synonyms None Definition None My comment: this term does not make any sense since the phage has the same integrase activity. This term should be made obsolete especially because it tends to be used for all integrases in bacterial genomes, many of which are not prophage-associated!
Accession GO:0009037 tyrosine-based site-specific recombinase activity Ontology molecular function Synonyms None Definition Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphotyrosyl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a tyrosine in the active site. [source: GOC:elh, PMID:11090626]
My comment: this defitnition is almost correct but should be seen in the context of a parent term such as "DNA breakage reunion activity". I presently have children for the term, to cover recombination leading to integration, excision or resolution. However a better solution may be to associate this activity with the processes integration, excision or resolution? Accession GO:0004803 transposase activity Ontology molecular function Synonyms None Definition Catalysis of the transposition of transposable elements or transposons. Transposases are involved in site-specific DNA recombination required for transposition in bacteria and other organisms. [source: ISBN:0198506732]
My comment: most transposases are DDE enzymes and hence are not site-specific recombinases (they rather use specific sites on the transposable element and random target sites!). So my definition, phi:0000153, DDE transposase activity (again under "DNA breakage reunion reaction/activity"): Catalysis of the transpositional recombination of a discrete DNA segment. DDE transposase have a related amino-acid motif (the DDE motif), which forms the active site of the transposase and is responsible for coordinating the cleavage and joining steps of transposition. Breakage of the DNA occurs at the end of the element (usually a hydrolysis) and is followed by breakage and integration at the target site (a transesterification reaction).
Accession GO:0045090 retroviral genome replication Ontology biological process Synonyms None Definition Any process involved in the replication of a retroviral genome. Retroviruses use RNA as their nucleic acid and reverse transcriptase to copy their genome into the DNA of the host cells chromosomes. [source: GOC:go_curators, ISBN:0198506732, http://cancerweb.ncl.ac.uk/]
My comment: this definition does not appear correct as the cDNA is not copied into the genome but copied and then integrated in the host genome to be transcribed/replicated. As it is now the retroviral integrase has no place to go!
Reported by: mah11
Original Ticket: "geneontology/ontology-requests/4256":https://sourceforge.net/p/geneontology/ontology-requests/4256