Phage call August 21st-23rd 2012
QUESTIONS FROM BRENLEY
- BM has been annotating phage lambda proteins (see Gene List of Lambda on EW). Problems I have encountered:
1/ 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
2/ 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 the current definition 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.
Changed definition to match Wikipedia: Icosahedral capsids have 12 pentamers and 10(T-1)hexamers, where T is the triangulation number.
3/ Need regulation of DNA integration terms -- GO:0015074 DNA integration
Becky has sent Brenley instructions for getting a TG1 login.
4/ Guess we need a terminase activity term (NOT specific to DNA or RNA!)
Becky to look into adding a terminase activity term (multi-functional enzyme, so would require two HAS_PART relationships for its separate functions).
5/ 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. Paola says: At our last apoptosis meeting, we agreed that "induction of apoptosis" terms could be merged with their parent "positive regulation of apoptosis" (apoptotic process to be precise). However, in looking more carefully at some annotations, we also realized that "induction of apoptosis" is often used to indicate the apoptotic process itself. Therefore we might end up proposing to merge "induction of apo." with "apoptotic process" itself. In the specific case of viral terms, the relevant annotations (if any) should help you decide. If no annotations, I'd go with merging with "apoptotic process". But please check with Jane in case I'm forgetting something (I have no specific notes on viral terms). Also, in case it may be useful (for other viral terms as well), there's this old-ish SF item: https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3317755&group_id=36855 Hope this helps, Paola
6/ Is it going to be confusing to have GO:0039633 killing by virus of host cells and cytolysis (i.e. both kill the cells)
Added relationship: killing by virus of host cell --[isa]cytolysis by virus of host cell
7 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?
After discussion with Jane: Changed definition of GO:0075733 intracellular transport of viral material to make it clearer that viral material means genome OR intact virus (virion). Made 'GO:0046788 egress of virus within host cell' a child of GO:0075733.
8/ 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.
9/ 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.
Added comment to 'induction by virus of host cell-cell fusion ; GO:0006948' to also consider 'spread of virus in multicellular host ; GO:0046739'.
10/ 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)
Doesn't sound to Becky like exocytosis is the way the holins work. Therefore added in P/F relationships: cytolysis by virus via pore formation in host cell membrane ; GO:0044660 --[partof]holin activity
11/ 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???
Discussed with Jane. 'lytic viral budding ; GO:0019078' is on Jane's obsoletion list. AI (JANE): Merge 'lytic viral release ; GO:0019077' with 'cytolysis by virus of host cell ; GO:0044659'.
12/ What happened to capsid formation around genome via self-assembly?
- Jane is working on these
13/ 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???
Added comment to GO:0019074 that the packaging can be ssRNA or dsRNA.
14/ I thought GO:0045090 retroviral genome replication was going away?
- on Jane's list for obsoletion
15. 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.
16. 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.
Added 'viral escort protein' as synonym for 'regulation of viral entry into host cell ; GO:0046596'.
17. How is GO:0042963 phage assembly separate from GO:0019068 virion assembly? They are the SAME!!
Merged 'phage assembly ; GO:0019068' into 'virion assembly ; GO:0019068'
18. 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???
AI (JANE): create relationship: 'provirus excision ; GO:0032359' is_a: 'release from viral latency ; GO:0019046'.
19. 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?
Added 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.
20/ 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.
21/ Is viral latency part of GO:0022611 dormancy process?
- dormancy is a developmental process. We all agree that viruses don't develop. 'viral dormancy' already exists as a synonym for 'viral latency ; GO:0019042', so nothing more to do here.
22/. I thought GO:0019038 provirus was going away???
- still there, but on the list for obsoletion
23. 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
- Is the viral nucleoid the region WITHIN the viral particle, or the region within the host cell????
- Presumably the nucleoid can contain either RNA or DNA? (the current definition is DNA-specific)
- NB: to create a viral-specific term, will need to redefine and rehouse the current 'nucleoid' term, out from under 'intracellular non-membrane bound organelle'.
- It seems that there's two ways in which the term 'nucleoid' is used, so will need 2 new terms:
- i) host cell viral nucleoid: the region in the host cell which contains the (actively replicating?) viral genome: RNA or DNA. is_a: host cell part.
- ii) virion nucleoid. The region within a viral particle in which the genomic material is housed (e.g. see HIV image).
created 2 new terms: virion nucleoid ; GO:0039642 host cell viral nucleoid ; GO:0039643
- 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