Phage call August 21st-23rd 2012

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QUESTIONS FROM BRENLEY

  • BM has been annotating phage lambda proteins (see Gene List of Lambda on EW)
  • problems I have encountered:
  • GO:0043493 viral terminase complex isn't under GO:0044423 virion part or better yet, 0019028 viral capsid
viral terminase complex ; GO:0043493
- host cell cytoplasm part
+ viron_part
  • GO:0019030 icosahedral viral capsid - definition is a bit confusing b/c it says "the subunits are arranged to form an icosahedron, a solid with 20 faces and 12 vertices".
 Changed definition to match Wikipedia: Icosahedral capsids have 12 pentamers and 10(T-1)hexamers, where T is the triangulation number.


    • Is that true always (i.e. pseudo-T3)? But there isn't an icosahedral viral capsid, major subunit... I just ran into this when annotating the major head protein of lambda (gpE). I could annotate to both (GO:0019030 and GO:0098017), but that seems kind of redundant.
  • need regulation of DNA integration terms -- GO:0015074 DNA integration
  • guess we need a terminase activity term (NOT specific to DNA or RNA!)

More issues from Bren

2. What is the difference between GO:0019051 induction by virus of host apoptotic process and GO:0060139 positive regulation of apoptotic process by virus? Why is 19 a child of 60? Are they not the same thing? 

Becky has emailed Paola, who's leading the apoptosis overhaul to check on what was decided about induction v pos regulation of apoptosis terms.

3. Is it going to be confusing to have GO:0039633 killing by virus of host cells and cytolysis (i.e. both kill the cells) 

Add relationship:
killing by virus of host cell
--[isa]cytolysis by virus of host cell


4. GO:0075733 intracellular transport of viral material – confusing without indicating mean genome in term & not viral procapsid transport term. Why is this separate from GO:0046788 egress of virus within host cell? 

Add relationship:
intracellular transport of viral material
--[isa]egress of virus within host cell

5. What about viral material transport out of nucleus? Does that happen through proteins???

  • leaving this for now - can add if people request terms for this.

6. Is GO:0006948 induction by virus of host cell-cell fusion related to GO:0046739 spread of virus in multicellular host?

  • the structure used for cell-cell fusion is not exclusively for spread.
Add comment to 'host cell-cell fusion' to also consider spread of virus term.


7. Should we add a comment to GO:0046756 lytic viral exocytosis about how this is how dsDNA phages get out (by encoding a holin & lysozyme), ssDNA and ssRNA phages (by preventing host PG biosynthesis)

  • should use lytic viral release, Becky making this new relationships for holin activity under this
    • Becky may link cytolysis and lytic viral release via new term
Add in P/F relationships for holins:
lytic viral release
--[partof]holin activity

or 

cytolysis by virus of host cell
--[partof]holin activity

create new term: lytic viral release by viral cytolysis of host cell ; GO:NEW

8. How does GO:0046754 non-lytic viral exocytosis work? Why is it different from GO:0046755 non-lytic virus budding (which says it is a form of viral envelopment)? Clarify that filamentous phage are the first & not the second in a comment???

  • defn of non-lytic exocytosis and release are basically the same thing, so what is the difference between those two terms & how does budding fit in???
  • ask Jane when she gets back!

9. What happened to capsid formation around genome via self-assembly?

  • Jane is working on these

10. Have to have a term for the dsRNA viruses that pack a SINGLE strand of RNA & then replicate in the head. OR clarify GO:0019074 viral RNA genome packaging to include this??? 

Add comment to GO:0019074 that the packaging can be ssRNA or dsRNA.

11. I thought GO:0045090 retroviral genome replication was going away?

  • on Jane's list for obsoletion

12. How is GO:0019081 viral protein biosynthetic process different from protein biosynthetic process? Is this the whole cellular problem???

  • discussing at Editors call, going to change the defintion of cellular in GO
  • separate cellular based on single or multi-organism processes.


13. Should there be “escort functions” for A2 and similar proteins that escort the genomes into the host & protect the genome from degradation???

  • similar to chaperone terms, no.
Add 'viral escort protein' as synonym for 'regulation of viral entry into host cell ; GO:0046596'.


14. How is GO:0042963 phage assembly separate from GO:0019068 virion assembly? They are the SAME!! 

Merge 'phage assembly ; GO:' into 'virion assembly ; GO:'

15. What is the difference between GO:0019046 release from viral latency and GO:0032359 provirus excision? Should GO:0032359 be a child of GO:0019046???

  • ask Jane when she gets back!

16. Does GO:0019066 translocation of virus into host cell for host proteins or the viral proteins that escort the genome into the cell? Does this need clarification? 

 Add comment to GO:0019066 that the term can be used to annotate viral escort proteins AND host proteins.
  • Becky will read up on escort proteins. Escort proteins protect the viral genome from degradation, but not sure on the mechanisms.

17. I think GO:0075001 adhesion of symbiont infection structure to host should have children viral attachment b/c the tail is a specialized structure meant to do that!

  • doesn't always hold true b/c some tails are single proteins (A, A2), and others don't even have tails.

18. Is viral latency part of GO:0022611 dormancy process?

  • ask Jane!
  • dormancy is a developmental process. Do viruses have developmental processes or do they only replicate??

19. I thought GO:0019038 provirus was going away???

  • still there, but on the list for obsoletion

20. New term -- GO:0009295 nucleiod -- child -- GO:00980xx ! virus nucleiod - The region of in the host cell to which viral DNA is confined.

  • Proteins (PhuZ) are responsible for centering the viral DNA for some bacterial viruses, Herpes virus, etc. PMID:22726436
  • Becky will look into adding a new term 'nucleoid' is_a: host cell part


Other stuff

  • I have GO:0098035 viral DNA genome packaging via site-specific sequence recognition (3’ and 5’ extensions) & GO:0098006 viral DNA genome packaging, headful
    • struggling to describe (CLEARLY) ways dsDNA genomes are packaged b/c others have terminal proteins that are bound to ends of replicated genome (NOT produced as a concatamer like site-specific dudes)
  • Linear vs Rotary motors???


  • Transposition, DNA mediated
    • replicative, non-replicative ok according to email exchange with Ariane T.
    • need term for class III -- BM
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