Virus ontology devt July 2012

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Overview

  • BM got the go ahead to work on this for the month of July 2012, so that started the project again
  • we need to fix the existing terms & relationships as well as add additional terms
  • Incorporating some MeGO terms

People

  • Jane Lomax, Rebecca Foulger, Brenley McIntosh

Timeline

  • July - devt
  • July 31st - 9am EST
    • Skype call to discuss
  • Aug 2nd - 8am EST
    • Skype call to discuss
  • Aug 9th - 10am EST
    • Skype again

Summary of Calls and Discussions


Change Parentage

  • GO:0060144 host cellular processes involved in virus induced gene silencing
  • GO:0015074 DNA integration
  • GO:0006310 DNA recombination


Clarify term or definition

Topics for Aug 21-23rd discussion

  1. GO:0043493 viral terminase complex isn't under GO:0044423 virion part or better yet, 0019028 viral capsid
  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 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.
  3. need regulation of DNA integration terms -- GO:0015074 DNA integration

Topics to cover for Aug 2nd discussion

  • new terms from BM
    • BM made transpososome, intasome, resolvasome, relaxosome complex terms, but should they all be grouped under recombination complex type term?
    • terminase activity (under GO:0015616)
    • viral membranes -- referred to by both camps (internal & external membranes)
    • capsid morphogenesis via nucleation? (TMV, HIV, L-A from yeast, MS2, etc)
    • RNA translocation terms ok?
  • replication tactics by viruses

Ontology cleanup & questions

  • 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.
    1. where is archaea cell surf bind?
    2. how are these terms not related? (Viruses bind all 3)
obsolete GO:0043498 and its children 
add child to GO:0046812 of host cell surface binding by virus or change the current term to include virus
  • GO:0008907 integrase activity & GO:0008979 prophage integrase activity
    • how are these diff other than a SO item?
problem with relationships between integrase being under cellular process currently
change to integrase activity involved in viral ....
  • 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

Stuck topics

  • term for post-segregational killing?
Jane - killing by virus of host cell by post-segregational killing.  add comment - occurs after plasmid partitioning
under GO:0001907
  • how do we handle exclusion? ('altruistic' -- doubly infected cells are killed) functions under GO:0039507 suppression by virus of host molecular function?
  • definition for GO:0005727 doesn't really work
its fine.
  • are the capsid terms I have ok with the wacky viruses (i.e. 5 morphologies of archaeoviruses)?
should be.  still question of dealing with core & outer capsid protein shells (Rotaviruses)
  • GO:0075529 establishment of latency as a circular episome
look good.
  • 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 syn???
  • I made structural molecule activity terms for virus proteins, but if we are going to obsolete them, is this bad???
these are ok
  • Is it bad that viral procapsid is under virion in CC tree?
its fine.
  • Can I just say GO:0009405 sucks?!?!?!
get examples for children
  • How do we handle Reoviruses (Rotaviruses) that have 2 concentric protein shells comprising its capsid? Ditto for phi6...

Topics to cover for July 31st discussion

  • 54 terms BM added to GO (some from MeGO, but not all)
  • BM rearranged a BUNCH of relationships
  • BM put in new MeGO dbxrefs for ~50 existing terms in GO


  • Things BM needs help with:
  • Where does restriction alleviation fit? (GO:0019048 virus-host interaction)
    • Change GO:0019049 evasion of host defenses by virus to suppression of ""
DONE (Becky). Changed to match parents and definition:
evasion by virus of host immune response ; GO:0030683
evasion of host defenses by virus ; GO:0019049
>
evasion or tolerance by virus of host immune response ; GO:0030683
evasion or tolerance of host defenses by virus ; GO:0019049


  • Where does lysis inhibition fit? (established virus vs newly-infecting virus in host?!)
    • response to virus -- suppression by virus of host cell lysis in response to superinfecting virus
  • Where does immunity fit? (lysogenized host is immune to superinfection)
    • add in immunity to viral latency definition
    • Jane has the latency terms
DONE (Jane). Added a whole bunch of new terms under 'viral latency ; GO:0019042' and fixed up defs etc.
  • Where does exclusion fit? (2 different viruses in same cell at same time = ONLY get progeny from 1)
    • BM will look into this & we will talk about it on Thurs
  • Are the MeGO terms for secretion system parts necessary?
    • No. Becky will add type V ss complex terms
DONE. Added:
type V protein secretion system complex ; GO:0098046
    • BM will look into shared parts of the ss
  • Do we want the specific children for the terminases, invertases, excisionases?
    • Becky will fix relationships for recombinases
NOT DONE IN THE END (Becky). I was going to add 
recombinase activity ; GO:0000150
--[isa]site-specific recombinase activity ; GO:0009009
BUT, the comment of GO:0009009 states: Note that this term is not a child of 'recombinase activity ; GO:0000150' because the latter represents activities that do  not break or form phosphodiester bonds. 
'GO:0000150' has a similar comment explaining the absence of the relationship, so I haven't added it in.


    • need children that are site-specific and not site-specific; then grandchildren are tyrosine, serine or DDE based
  • How do excisionase and invertase and integrase fit into DNA cleavage activities or are they separate?
    • Becky will do process:function relationships for these
DONE. Added P/F relationships as follows:
DNA integration ; GO:0015074
--[part_of]integrase activity ; GO:0008907
DNA recombination ; GO:0006310
--[part_of]recombinase activity ; GO:0000150
BUT... the GOEds need to look at the cellular parentage of the DNA metabolism terms. Causes disjoint TPVs when a protein metabolises the DNA of another organism. Several of the definitions & synonyms of child terms will be affected.

  • Should we include the complexes transpososome, intasome, resolvasome, relaxasome?
done.  BM will send tomorrow. 
  • How do we describe the injected proteins?
    • not in scope of GO directly
    • functions possible -- RNA binding involved in genome entry into host cell
    • what are the types of proteins?? BM will find out.
  • What should the definition of terminase activity be? Is it necessary?
done.  BM will send tomorrow.
  • Need to redefine GO:0046797, GO:0019061 & GO:0004803.
  • Is GO:0098034 ok?
  • What do we do with the plasmid virus terms?
    • new terms by Jane suit these fine
  • What do we do with replication by transposition terms?
    • has part transposition, DNA-mediated (GO:0006313)
    • under viral genome replication (BM)
  • How do we handle the viral envelopes since some are INTERNAL, others are EXTERNAL, but the current defn is only for EXTERNAL?
    • merge virion membrane and viral envelope & make children for internal and external
 HELD OFF on the merge because I see viral membranes crop up again for our Thursday session.
  • What do we do with GO:0009293 (transduction) and children from BM?
    • toss it. obsolete.

More discussion

  • GO:0060144 - needs to be under multi-organism process
DONE (Jane). Fixed immediate parentage issue. Although virus-induced gene silencing is something that really needs looking at in more detail - the terms we have are really outdated with recent developments - RNAi etc. And in fact virus-induced gene silencing is now only ever mentioned as a technology rather than a biological process, so these terms are extra confusing. I'll make a SF ticket.



    • Jane
  • capsid self-assembly term
    • under viral capsid assembly


EDITS DONE

EDITS DONE BY JANE

New terms:

  • GO:0044659 cytolysis by virus of host cell & children
  • GO:0044662 disruption by virus of host cell membrane
  • GO:0098046 type V protein secretion system complex
  • GO:0019042 viral latency & children



EDITS: AUGUST 6TH, BECKY

Added new terms that Brenley had created in OBO-Edit. At the August 2nd jamboree, Jane, Becky and Brenley went through these terms and tweaked the names, definitions and position where necessary.

name: virus tail assembly ; GO:0098003
name: virus tail fiber assembly ; GO:0098004
name: virus head-tail joining ; GO:0098005
name: viral DNA genome packaging, headful ; GO:0098006
name: virus terminase, large subunit ; GO:0098009
name: virus tail ; GO:0098015
name: viral capsid, major subunit ; GO:0098017
name: viral capsid, minor subunit ; GO:0098018
name: virus tail, major subunit ; GO:0098019
name: virus tail, minor subunit ; GO:0098020
name: viral capsid, decoration ; GO:0098021
name: viral capsid, fiber ; GO:0098022
name: virus tail, tip ; GO:0098023
name: virus  tail, fiber ; GO:0098024
name: virus tail, sheath ; GO:0098027
name: virus tail, shaft ; GO:0098028
name: icosahedral viral capsid, spike ; GO:0098029
name: icosahedral viral capsid, neck ; GO:0098030
name: icosahedral viral capsid, collar ; GO:0098031
name: icosahedral viral capsid, collar fiber ; GO:0098032
name: icosahedral viral capsid, neck fiber ; GO:0098033
name: viral DNA genome packaging via site-specific sequence recognition ; GO:0098035
name: viral DNA genome packaging, 3' extended cos packaging ; GO:0098036
name: viral DNA genome packaging, 5' extended cos packaging ; GO:0098037
name: non-replicative transposition, DNA-mediated ; GO:0098038
name: replicative transposition, DNA-mediated ; GO:0098039
name: virus baseplate assembly ; GO:0098045
name: viral capsid, internal space ; GO:0098061
name: RNA translocase activity ; GO:0039630
ID: GO:1901217 Label: regulation of holin activity
ID: GO:1901218 Label: negative regulation of holin activity
DNA translocase activity involved in viral DNA genome packaging ; GO:0039631
RNA translocase activity involved in viral RNA genome packaging ; GO:0039632
  • Changed 'GO:0019049 evasion of host defenses by virus' to 'evasion or tolerance of host defenses by virus ; GO:0019049'


EDITS: AUGUST 10TH, BECKY

new terms:

killing by virus of host cells ; GO:0039633
killing by virus of host cells during superinfection exclusion ; GO:0039634
suppression by virus of host peptidoglycan biosynthetic process ; GO:0039635
suppression by virus of host cell wall biogenesis ; GO:0039636
catabolism by virus of host DNA ; GO:0039637
  • Added comment to 'genetic transfer ; GO:0009292' that it doesn't include lysogeny. GO:0009292 should not be used for annotation of phage lysogeny (integration of the bacteriophage nucleic acid into the host bacterium's genome).
  • Added comment to 'mating ; GO:' to consider instead using 'conjugation ; GO:0000746': For single-celled organisms, consider instead annotating to 'conjugation ; GO:0000746' or its children.
  • Deleted following relationship because a virus responding to another virus can be annotated with GO:0009597: added a comment to make this clearer.
detection of symbiont ; GO:0009602
--[isa]detection of virus ; GO:0009597
  • Tweaked definition of transposase activity ; GO:0004803 to make it clearer that the enzyme is site-specific for viral DNA/element but isn't always site-specific for the host DNA insertion site.
  • Created relationship:
adhesion of symbiont to host cell ; GO:0044650
--[isa]viral attachment to host cell ; GO:0019062
  • Added to comment of 'growth of symbiont in host cell ; GO:0044119' that the term is not suitable for viral replication in a host cell.



ACTION ITEMS

ACTION ITEMS FOR JANE

  • GO:0046739 spread of virus in host -- change to spread of virus in multicellular host


OBSOLETIONS_TO_DO (JANE)

  • GO:0045090 retroviral genome replication & its children (JANE)
    • ultimately, not different from processes already described in GO & we aren't delineating between the types of viruses, only the attributes of the gene products
  • GO:0019038 provius
    • SO term, not GO
  • GO:0009293 transduction
    • per Jim Hu sourceForge item - not clear what gp you would annotate to this -- it is more a process characterizing phage
  • GO:0043498 cell surface binding & its children
    • already have host cell surface binding
  • genome types (DNA, RNA) in cellular component tree.


ACTION ITEMS FOR BECKY

  • DNA recombinase mediator complex ; GO:0033061
    • Request from Brenley to make the complex annotatable to Prokaryotes too.
    • See SF item for issues (including current nuclear parentage) [1]


ACTION ITEMS FOR BRENLEY

  • Ask Arrianne exactly what is the difference btwn rolling circle transposition & conservative transposition?!


UNRESOLVED ISSUES

  1. capsid self assembly (under virus capsid assembly)
  2. viral membranes
  3. GO:0000150 recombinase activity -- relationships
  4. GO:0033061 DNA recombinase mediator activity -- definition includes nuclear localization (not in prok/arch), but will change a bunch of relationships...
  5. GO:0008907 integrase activity (GO:0008979 prophage integrase activity) -- cellular process
  6. Spanins and Holins (see below)


SPANINS AND HOLINS

  • Jim is VERY VERY VERY keen that we don't obsolete the current holin terms. Becky volunteered from the 31st July jamboree to go away and look at the holin and spanin terms. Her suggestions are below.
  • Do we want the children of spanin terms? At the least, the defn for spanin in MeGO needs to be altered.
  • We may be able to put a process terms for spanin under 'disruption by symbiont of host cell (GO:0044004)' - Jane


HOLINS

Background to what holins do:

  • essential for host lysis by bacteriophage.
  • small membrane proteins
  • accumulate in membrane then act to permeabilize the membrane (by making themselves into a hole). Permealized either to an endolysin, so the endolysin can reach the cell wall and degrade it (thus the holin controls the functional access of the endolysin to the murein) or to ions to cause a collapse of the membrane potential.
  • Doesn't appear to be known if the hole is just a hole, or an actual channel.
  • Holins act as 'clocks' and only make the holes when the time is right. Not sure how this is judged yet.
  • If the holins are not considered to be channels (see question below), there's no suitable function term, short of 'hole activity'. Therefore, I propose to obsolete the existing 'holin activity' terms, and replace them with new process terms. We've tried obsoleting 'holin' twice before, but it's still managed to stay in the ontology with 'activity' bunged on the end... sneaky. Here's my suggestion... let me know if it works for you:
obsolete: 
holin activity ; GO:0034290
canonical holin activity ; GO:0034291
pinholin activity ; GO:0034292
Reason for obsoletion: These terms represent a family of proteins and not an activity. Replacement terms are suggested below.
Add new terms:
regulation of plasma membrane permeability ; GO:NEW1
negative regulation of plasma membrane permeability ; GO:NEW2
positive regulation of plasma membrane permeability ; GO:NEW3
plasma membrane permeabilization involved in cytolysis by virus of host cells ; GO:NEW4
plasma membrane permeabilization to endolysin involved in cytolysis by virus of host cells ; GO:NEW5
plasma membrane permeabilization to ions involved in cytolysis by virus of host cells ; GO:NEW6

Definitions of new terms:

regulation of plasma membrane permeability ; GO:NEW1
Any process that modulates the frequency, rate or extent of the passage or uptake of molecules by a plasma membrane.
is_a: regulation of biological quality ; GO:0065008
is_a: plasma membrane organization ; GO:0007009
(Similar for negative and positive children)
plasma membrane permeabilization involved in cytolysis by virus of host cells ; GO:NEW4
synonym: holin-mediated permeabilization [EXACT?]
synonym: holin-dependent membrane permeabilization [EXACT?]
synonym: positive regulation of plasma membrane permeability involved in cytolysis by symbiont of host cells [EXACT]
synonym: cytoplasmic hole formation during host lysis by bacteriophage [NARROW? or EXACT?]
synonym: holin activity [RELATED]
The temporally-regulated permeabilization of the host plasma membrane (cytoplasmic membrane) by a virus/bacteriophage during lysis of the host cell.
Comment: The transmembrane holin proteins accumulate in the membrane of the host cell, and at a specific time point form a hole through the cytoplasmic membrane  that allows the passage of enzymes and/or other molecules to lyse the host cell.
plasma membrane permeabilization to endolysin involved in cytolysis by virus of host cells ; GO:NEW5
The temporally-regulated permeabilization of the plasma membrane (cytoplasmic membrane) to a fully-folded phage-encoded endolysin (murein-degradase), so the  endolysin can reach and degrade the murein within the cell wall during lysis of the host cell by a virus.
exact synonym: endolysin-specific hole formation during host cell lysis by bacteriophage
synonym: canonical holin activity [RELATED]

plasma membrane permeabilization to ions involved in cytolysis by virus of host cells ; GO:NEW6
The temporally-regulated permeabilization of the plasma membrane (cytoplasmic membrane) to ions, causing irreversible depolarization of the cell membrane and lysis of the host cell by a virus [PMID 19861547].
synonym: hole formation during host cell lysis by bacteriophage [EXACT?]
synonym: pinholin activity [RELATED]


QUESTIONS ON HOLIN TERMS:

  • QUESTION 1: membrane organization is under 'cellular process'… this is going to cause problems again, isn't it.
  • QUESTION 2: wrt whether the synonyms should be exact or narrow, would you use these terms to annotate anything other than holins?
  • QUESTION 3: wrt definitions & synonyms, is this process specific to bacteriophages?
  • QUESTION 4: Am I right in saying that it's the plasma membrane (equivalent to the cytoplasmic/inner membrane in bacteria) that the holes are formed in?
  • QUESTION 5: Would you say that a holin should be annotated to 'channel activity'?

SPANINS

Background to what spanins do (PMID 20734329):

  • Acts at the 3rd step in lysis (acting after holins and endolysins): involved in disrupting the outer membrane (OM).
  • span the periplasm
  • form dimers and monomers
Add new terms:
disruption by virus of host cell outer membrane ; GO:NEW
disruption by virus of host cell outer membrane involved in cytolysis by virus of host cells ; GO:NEW 
New term definitions:
disruption by virus of host cell outer membrane ; GO:NEW
A process by which a virus has a negative effect on the functioning of the host's cell outer membrane. The cell outer membrane is a lipid bilayer that forms the  outermost layer of the cell envelope.
disruption by virus of host cell outer membrane involved in cytolysis by virus of host cells ; GO:NEW 
A process by which a virus has a negative effect on the functioning of the host's cell outer membrane that contributes to lysis of the host cell.
synonym: spanin activity [RELATED]
synonym: OM disruption during cell lysis [PMID: 20734329]
comment: Consider also annotating to 'host cell periplasmic space ; GO:0044229'


QUESTIONS ON SPANIN TERMS:

  • QUESTION: Do you know HOW the spanins disrupt the outer membrane? Is it just by being wedged in the periplasmic space? Might be by fusing the OM with the plasma membrane (PMID 20080651)