#10002 protein-nucleic acid complex displacement activity

open
David Hill
5
2013-02-21
2013-02-20
Jim Hu
No

Based on http://www.genesdev.org/cgi/doi/10.1101/gad.1684008.

The authors show that the B subtilis DNA translocase SpoIIIE acts as a "wire stripper" to remove proteins from DNA as it transports DNA from the mother cell to the forespore. I'm thinking this might represent a class of activities, and terms could be vlable for capturing disinctions between proteins that are or are not blocked in their movement on nucleic acids by protein roadblocks. I think there are three things that can happen
- the moving protein is roadblocked
- the moving protein displaces the roadblock
- the moving protein bypasses the roadblock
I believe all three have been observed for translocases, helicases, and polymerases.

A problem I see is that some proteins may act differently depending on the nature of the roadblock.

Discussion

  • David Hill
    David Hill
    2013-02-21

    Hi Jim,

    I think it is ok if the proteins act differently. That would be captured at the level of the annotation. For the new terms in the ontology, we would want to list and categorize the activities themselves. Can you suggest some term names for the activities of this class of proteins?

    David

     
  • David Hill
    David Hill
    2013-02-21

    • assigned_to: nobody --> ukemi
     
  • Jim Hu
    Jim Hu
    2013-02-21

    I was thinking of something as simple as

    protein-nucleic acid complex displacement activity
    |_protein-DNA complex displacement activity
    |_protein-RNA complex displacement activity

    That's trying to use our style of ending everything with "activity". A more natural set of names might be:

    displacement of protein-nucleic acid complexes
    |_displacement of protein-DNA complexes
    |_displacement of protein-RNA complexes

    I would want some way in the definition or ontology structure to distinguish these from some of the complex disassembly terms, because I think these are different.

    For the other outcomes (blockage and bypass), I'm not sure how the ontology would capture these because the outcome is sometimes more property of the roadblock complex rather than the protein that is trying to get past it. Or it's a property of the collection of participants. There may be some process terms that would be applicable, but I'm not sure. For example, there may be proteins required for reassembly of chromatin as replication forks pass through. IIRC, the epigenetic patterns of histone modificaitons are preserved based on how this works. Perhaps someone like Karen could comment on how this is expressible or not in GO.

    Is that responsive to your question?

    Jim

     
  • David Hill
    David Hill
    2013-02-21

    Hi Jim,

    Thanks for the quick response. What if I make them children of the appropriate 'macromolecular complex subunit organization' terms? From the abstract, the paper describes the activity wrt DNA. Is there proof that the RNA activity exists too?

    Another thought was to make these activities children of negative regulation of binding terms, but that doesn't quite sit well with me.

    I think for now, we can leave the process links out.

    David