quer: function in process? DNA restriction

[gocentral]

GO:0009307

The cleavage of DNA by restriction nucleases, which cut the DNA double helix at specific sites defined by the local nucleotide sequence.

isn't this a nuclease?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/2415":https://sourceforge.net/p/geneontology/ontology-requests/2415

[gocentral]

Logged In: YES user_id=482944

Hello,

Yes, I guess technically this does correspond to a function. However, the term DNA restriction refers to the DNA restriction/modification systems of bacteria which protect the cells from invading foreign DNA. Although the restriction part of the system is a nuclease, I think there is value in being able to know that this nuclease is part of a restriction system and that there is more information conveyed with the restriction process then with just the function. Perhaps the definition needs to be expanded to include more information?

Michelle

Original comment by: mlgwinn

[gocentral]

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Ok thanks Michelle that makes sense. I notice Interpro have mapped dicer to this term, which will be outside of the scope of this term if the definition is updated.

I'll make a SF entry on the annotation tracker to remove the mapping.

Thanks

Val

Original comment by: ValWood

[gocentral]

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Hi Val,

As I think about this more - I wonder if the term shouldn't be "DNA restriction-modification system" instead of just DNA restriction. I think there used to be a similar term, but it was removed, if I remember correctly. That way there would be no confusion and one would be able to immediately pull out all the enzymes involved in the system both the nuclease and the methylases, whereas now, the restriction/modification methylases will be mixed in with all the other ones in "DNA methylation" or "DNA modification".

What do you folks in the GO office think?

Michelle

Original comment by: mlgwinn

[gocentral]

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I can't find any indication in the email archive or the ontology diffs to suggest that we once had a 'restriction/modification' term. It seems reasonable to have such a term, since it's a genuine biological process that integrates methylation of 'self' DNA and cleavage of 'other' DNA.

We can reword the name and definition of the existing term, GO:0009307, as long as it's still going to be consistent with existing annotations. There are over 3400 (!!), so it would really be a pain to make GO:0009307 obsolete. I'm not so worried about the interpro2go mappings, because they can just be fixed (tho I can't tell from the mappings why they'd map dicer anyway... the interpro entries in the file all seem to be individual restriction endonucleases ...).

We should notify the mailing list, though, before we do anything, because so many annotations are involved.

As a picky detail, we would prefer the hyphenated version of the term name, because we're trying to minimize the use of slashes.

m

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> 224410

Original comment by: mah11

[gocentral]

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I've notified the list that I will rename GO:0009307 and alter the wording of the def, unless anyone squawks within a week.

How would this do for a new def? The processes that protect an organism from invading foreign DNA by methylation of self DNA at specific sequences and nucleolytic cleavage of unmethylated foreign DNA. [GO:mah]

m

Original comment by: mah11

[gocentral]

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Hi Midori,

I like your definition. Your plan sounds good to me.

Michelle

Original comment by: mlgwinn

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Logged In: YES user_id=436423

Both changes made as described.

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11