Phage call August 21st-23rd 2012

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Topics for Aug 21-23rd discussion


  • 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
  • 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".
    • 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?

  • Paola reorganized the apoptosis terms, so Becky with check with her. Before, induction was a specific kind of positive regulation.

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)

  • Becky will make cytolysis a kind of KILLING

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?

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.

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

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???

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

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

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

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

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???

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?

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!

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

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

Other stuff

1. GO:0046729 spread of virus in host

  • change to spread of virus in multicellular host?

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

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

  • 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???


  • killing by virus of host cells during superinfection exclusion ; GO:0039634
    • 1/ Is it ALWAYS a lysogenic virus that kills the host cell in response to a subsequent lytic viral infection?
    • PMID: 22398285 suggests that the second virus can be the same or a closely related viral type.
  • Do we need a term for SUPERINFECTION EXCLUSION (where a pre-existing virus prevents infection of a host cell by a second virus).