Phage call August 21st-23rd 2012: Difference between revisions
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1. GO:0046729 spread of virus in host | 1. GO:0046729 spread of virus in host | ||
* change to spread of virus in multicellular host? | * change to spread of virus in multicellular host? | ||
* done | |||
11. I thought GO:0045090 retroviral genome replication was going away? | 11. I thought GO:0045090 retroviral genome replication was going away? | ||
* Jane is doing these. | |||
19. I thought GO:0019038 provirus was going away??? | 19. I thought GO:0019038 provirus was going away??? | ||
* still there... | |||
* obsolete. | |||
Revision as of 11:17, 23 August 2012
Topics for Aug 21-23rd discussion
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
- 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???
- Becky will add comment that the packaging can be ssRNA or dsRNA or dsDNA.
11. I thought GO:0045090 retroviral genome replication was going away?
- obsolete request going to go out from Jane
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 process
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.
- synonym for GO:0046596 of viral escort (hopefully will point people here)
14. How is GO:0042963 phage assembly separate from GO:0019068 virion assembly? They are the SAME!!
- Becky is merging phage assembly into virion assembly
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?
- for both (host & virus) - Becky will add comment
- Becky will read up on escort proteins
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?
- for Jane!
- dormancy is a developmental process. Do viruses have developmental processes or do they only replicate??
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 add.
Other stuff
1. GO:0046729 spread of virus in host
- change to spread of virus in multicellular host?
- done
11. I thought GO:0045090 retroviral genome replication was going away?
- Jane is doing these.
19. I thought GO:0019038 provirus was going away???
- still there...
- obsolete.
- 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???
QUESTIONS FROM BECKY
- 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).