mp: GO:0009009 : site-specific recombinase activity

[gocentral]

Hello,

GO:0009009 : site-specific recombinase activity should be a child of

GO:0000150 : recombinase activity

I think

Pascale

Reported by: pgaudet

Original Ticket: "geneontology/ontology-requests/3932":https://sourceforge.net/p/geneontology/ontology-requests/3932

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I'm getting myself confused by the definitions, so I'll ask Eurie to look.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=554670 Originator: NO

Here's the mini-summary of the difference of the two:

site-specific recombinases recognize short specific sequences and create new phosphodiester bonds between strands of DNA. This is definitely a catalytic activity.

recombinases just recognize homologous sequences between two strands of DNA. these regions can be quite long.

I'm not entirely comfortable with site-specific being a child of recombinase. Siblings yes... Here are some rambling thoughts why:

Should recombinase even be a child of "catalytic activity" because it doesn't necessarily break any chemical bonds - it might disrupt hydrogen bonds between base pairs. Is that enough to mandate a "catalytic activity" parent?

The common thing they share is the ability to recognize homologous regions of DNA but what they do with it is different. Is there some sort "nucleic acid pairing" function term? That would be an appropriate parent term for both.

If not, both GO:0000150 : recombinase activity and GO:0009009 : site-specific recombinase activity should be a child of 'DNA binding'. And site-specific recombinase could keep its catalytic activity parentage.

What do you think?

Original comment by: eurie

[gocentral]

Logged In: YES user_id=803460 Originator: YES

Hi Eurie,

Thanks for taking the time to answer this. What happened is that I opened the 'catalytic activity' node it it looked very untidy... Also, for naive people it's rather unintuitive that site-specific recombinase is not a kind of recombinase. Is there another way to phrase this you think?

I'll look into it more tomorrow.

Pascale

Original comment by: pgaudet

[gocentral]

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Eurie - Thanks for the explanation; I don't feel so bad about being confused now!

I see why GO:0009009 should not be a child of GO:0000150; the names are kind of confusing but if that's what's used in the community and literature, we can live with it. I do recommend adding comments to capture the distinction and explain why we haven't made the relationship. I'll follow your lead on whether to leave recombinase (GO:150) under catalytic activity or not ... but I think helicases are under catalytic activity, so there's precedent.

> Is there some sort "nucleic acid pairing" function term?

Not yet, but I believe Karen C has something in the works; see SF 1585409. I imagine there will be relationships to nucleic acid binding and/or its children, as appropriate.

https://sourceforge.net/tracker/index.php?func=detail&aid=1585409&group\_id=36855&atid=440764

m

Original comment by: mah11

[gocentral]

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I did some pubmed and google searches to try to find out alternate wordings to make it more clear but these two are the most commonly used for these function. There is some use of the synonym "strand transferase" for GO:0000150 : recombinase activity but it looks like it's often used when a protein appears to have that activity possibly as an artifact.

I think a comment might be the way to go. Let me know if you need me to write up something more eloquent or if my chicken scratch is enough.

If helicases are below catalytic activity, then it's probably ok. It's an energy dependent process. When there are "nucleic acid pairing" terms, then we can move these over.

Original comment by: eurie

[gocentral]

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OK thanks for clarifying this. You can close the issue.

Pascale

Original comment by: pgaudet

[gocentral]

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I've added comments to GO:0000150 and GO:0009009.

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori
• status: open --> closed-works-for-me

Original comment by: mah11