Phage jamboree- II August 2nd 2012

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PHAGE JAMBOREE NUMBER 2: AUGUST 2ND 2012

Present:

  • Brenley
  • Jane
  • Becky
  • Shabnam


Questions from Brenley on her new terms

  • BM made transpososome, intasome, resolvasome, relaxosome complex terms, but should they all be grouped under recombination complex type term?
    • Come back to on later August call once Brenley has looked at these some more.
  • terminase activity (under GO:0015616)
    • Terminases are multifunctional enzymes, so this may be better captured at the annotation level. Becky and Jane will bring up at an editors meeting what the best way to handle these multifunctional enzymes is.
  • viral membranes -- referred to by both camps (internal & external membranes)
    • Come back to viral membranes and viral envelopes.
  • capsid morphogenesis via nucleation? (TMV, HIV, L-A from yeast, MS2, etc)
    • Brenley has suggested the term: name: viral RNA genome packaging, nucleation ; GO:0098034
    • JANE TO LOOK AT AND ADD… self-assembly.
  • RNA translocation terms ok?
    • Becky added 'RNA translocase activity ; GO:0039630'. (see text file from Brenley with her terms in)
  • replication tactics by viruses


Questions from Brenley on Existing Terms

  • under binding, there is GO:0043498 cell surface binding (and its children bact cell surf bind & euk cell surf bind), then GO:0046812 host cell surface binding and GO:0001530 lipopolysaccharide binding. Why are these terms not related?
    • Becky to make new terms: 'LPS binding involved in viral attachment to host cell ; GO:NEW', and 'receptor binding involved in viral attachment to host cell ; GO:NEW'.
    • Jane to obsolete: bacterial cell surface binding ; GO:0051635, and eukaryotic cell surface binding ; GO:0043499. Use annotation extension column instead to capture this information.
  • GO:0008907 integrase activity & GO:0008979 prophage integrase activity. How are these diff other than a SO item?
    • There's a problem with integrase activity being under cellular process currently. Jane and Becky will bring up the cellular problem at the next editors call.
    • Add relationships and synonyms to 'GO:0008979 prophage integrase activity': integrase activity involved in establishment of integrated proviral latency.
  • GO:0000150 recombinase activity has child GO:0009009 site-specific recombinase activity.
    • first, can we use this to fix transposases? (children would be serine-based and tyrosine-based transposase, with child under tyrosine of Y2 transposase activity)
    • second, can we add non-site-specific recombinase activity with child DDE-based recombinase activity + child under GO:0009009 serine-based recombinase activity?
nevermind


Other Questions from Brenley

  • Can we have a term for post-segregational killing?
    • Jane - Add term under GO:0001907: 'killing by virus of host cell by post-segregational killing'. Add comment that it occurs after plasmid partitioning.
  • how do we handle exclusion?
    • Becky added term: killing by virus of host cells during superinfection exclusion ; GO:0039634
  • definition for 'extrachromosomal circular DNA ; GO:0005727' doesn't really work.
    • Decided this was fine.
  • are the capsid terms I have ok with the wacky viruses (i.e. 5 morphologies of archaeoviruses)?
    • Should be: just annotate to the structures that are applicable. There's still the question of dealing with core & outer capsid protein shells (Rotaviruses).
  • GO:0075529 establishment of latency as a circular episome
    • Looks fine.
  • How do GO:0046739 spread of virus in host, & GO:0019089 transmission of virus & GO:0046794 virion transport relate?
    • Need to change GO:0046729 to spread of virus in multicellular host.
    • Phages would be annotated to transmission of virus and not spread of virus in multicellular host
  • How are we handling DNA replication being a cellular macromolecule biosynthetic process & is that why GO:0019081 viral protein biosynthetic process is its own term even though the syn of viral proteins isn't different from any other form of protein synthesis???
  • Is it bad that viral procapsid is under virion in CC tree?
    • Its fine.
  • Can I just say 'pathogenesis ; GO:0009405' sucks?!?!?!
    • Brenley to get examples for child terms.