DNA geometric change Parents/children

[gocentral]

DNA geometric change is a child of DNA metabolic process

but not all DNA geometric change is necessarily metabolic

At present

DNA metabolic process --DNA geometric change ----DNA duplex unwinding (only child)

but possibly DNA bending could be a sibling and this is not mecessarily DAN metabolic process

in this case perhaps

DNA metabolic process --DNA duplex unwinding DNA geometric change --DNA duplex unwinding --DNA bending (GO new) or GO:0008301 DNA bending activity The function of causing local conformational micropolymorphism of DNA in which the original B-DNA structure is only distorted but not extensively modified. shoud perhaps be a process term ?

(I don't think we would consider DNBA bending as DNA metabolicm, but it is geometric change)

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/6596

[gocentral]

Another consideration, there is also a term DNA topological change. Should this be a child of DNA geometric change also.

Original comment by: ValWood

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: jenclark

[gocentral]

A bit of confusion seems to have arisen in the "matrix" email thread. DNA topological change is NOT a type of DNA geometric change.

Background: A closed circular DNA molecule, or a linear molecule in which the ends are physically constrained (or so distant that they're effectively constrained) has three attributes, twist (Tw), writhe (Wr), and linking number (Lk), related by

Lk = Tw + Wr

There's a decent summary in the introduction of this paper: http://www.ncbi.nlm.nih.gov:80/pmc/articles/PMC2662687/

A topological change occurs, by definition, when the linking number changes; Lk can only be changed by breaking and re-forming bonds (this is what topoisomerases do), so topological change does fit neatly under DNA metabolism.

A geometric change is one that changes twist and writhe without changing Lk.

I'm inclined to agree that DNA geometric changes aren't always metabolism, assuming that we take "metabolism" to involve forming or breaking chemical bonds. That means we have to put the term somewhere else, and at the moment I don't see anything better than 'cellular process'. I've dredged up email saying that at the time that we added 'DNA geometric change' we also thought " would be nice to have a parent for geometric+topological change, but we don't know what to name it". I could use 'DNA conformation change' as suggested back then.

Some other possible geometric changes are mentioned in papers such as: http://tfiib.med.harvard.edu/bcmp200/readings/condensin.pdf

... although we don't have terms for anything other than unwinding.

I've been trying to figure out whether DNA bending always changes twist and/or writhe, but am still not sure, so if we did have a process term, I'd be reluctant to put it under DNA geometric change. Lk, Tw, and Wr, and therefore geometric and topological changes, get talked about in the context of circles and constrained-end linear molecules, whereas bending can also affect linear molecules with free ends. In any case, I think it makes sense to keep the GO MF term, but we can probably get along fine without a BP term.

m

Original comment by: mah11

[gocentral]

OK I agree. The main issue is that DNA geometric change should move from under DNA metabolism as this is not always true.

val

Original comment by: ValWood

[gocentral]

OK, fixed now. I added DNA conformation change GO:0071103, and made it the only parent of geometric change, and an additional change for topological change and DNA packaging.

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> 224410
• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11