New phage terms mapping to SPKW/ViralZone

[gocentral]

UniProt have sent us a set of new phage KWs and ViralZone terms that they have added in collaboration with Ariane Toussaint. The idea was to cover all main molecular mechanisms and structural elements for phages.

The mapping file is attached. We should add GO terms to map to the new phage terms where appropriate and add to the spreadsheet so UniProt can do reciprocal mappings.

Reported by: jl242

Original Ticket: geneontology/ontology-requests/11251

[gocentral]

I've moved this to a GoogleDoc for ease:

https://docs.google.com/spreadsheets/d/1lWYDJafaV1ebI13-nVDD0wO3I-TD2do1QYCHRW75biY/edit?usp=sharing

Original comment by: jl242

[gocentral]

Original comment by: jl242

[gocentral]

• assigned_to: Jane Lomax --> David Osumi-Sutherland

Original comment by: jl242

[dosumis]

ViralZone terms added so far (DOS 2016):

[Term] id: GO:0098931 name: virion attachment to host cell flagellum namespace: biological_process def: "The process by which a virion attaches to a host cell by binding to the flagellum of a cell surface." [GOC:dos, VZ:3949] subset: virus_checked xref: VZ:3949 "Pilus-mediated viral adsorption onto host cell" is_a: GO:0019062 ! virion attachment to host cell

[Term] id: GO:0098932 name: disruption by virus of host cell wall petidoglycan during virus entry namespace: biological_process def: "A process carried out by a symbiot that breaks down peptidoglycans in the cell wall of its host . The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:dos, VZ:3940] subset: gosubset_prok synonym: "catabolism of host cell wall peptidoglycan by organism" EXACT [] synonym: "degradation of host cell wall petidoglycan by organism" EXACT [] synonym: "degradation of host peptidoglycans during virus entry" EXACT [VZ:3940] synonym: "disassembly by organism of host cell wall peptidoglycan" EXACT [] synonym: "disassembly by symbiont of host cell wall peptidoglycan" EXACT [] xref: VZ:3940 is_a: GO:0044661 ! disruption by virus of host cell is_a: GO:0052009 ! disruption by symbiont of host cell wall relationship: part_of GO:0046718 ! viral entry into host cell

[Term] id: GO:0098933 name: disruption by symbiont of host cell envelope namespace: biological_process def: "The breakdown of the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684] subset: gosubset_prok synonym: "catabolism of host cell wall by organism" EXACT [] synonym: "degradation of host cell wall by organism" EXACT [] synonym: "disassembly by organism of host cell wall" EXACT [] synonym: "disassembly by symbiont of host cell wall" EXACT [] is_a: GO:0052008 ! disruption by symbiont of host cellular component is_a: GO:0052020 ! modification by symbiont of host cell wall is_a: GO:0052339 ! disruption by organism of cell wall of other organism involved in symbiotic interaction

Term] id: GO:0098994 name: disruption of host cell envelope during viral entry namespace: biological_process def: "The disruption of host cell wall by viral proteins during virus entry" [GOC:dos] synonym: "catabolism of host cell wall during viral entry" EXACT [] synonym: "degradation of host cell envelope components during virus entry" EXACT [VZ:3938] synonym: "degradation of host cell wall during viral entry" EXACT [] synonym: "disassembly of host cell wall during viral entry" EXACT [] xref: VZ:3938 is_a: GO:0098933 ! disruption by symbiont of host cell envelope intersection_of: GO:0098933 ! disruption by symbiont of host cell envelope intersection_of: part_of GO:0046718 ! viral entry into host cell

[Term] id: GO:0098995 name: disruption by virus of host envelope lipopolysaccharide during virus entry namespace: biological_process def: "The breakdown of lipopolysaccharides in a host cell envelope during virus entry into a host cell. For example a phage entering a gram-negative bacterium may actively break down outer membrane lipopolysaccharides." [GOC:dos, VZ:3940] subset: gosubset_prok synonym: "catabolism of host cell wall peptidoglycan by organism" EXACT [] synonym: "degradation of host cell envelope lipopolysaccharide during viral entry" EXACT [] synonym: "degradation of host lipopolysaccharide during virus entry" EXACT [VZ:394] synonym: "disassembly by virus of outer membrane lipopolysaccharide during viral entry" NARROW [] xref: VZ:3939 is_a: GO:0044661 ! disruption by virus of host cell is_a: GO:0052009 ! disruption by symbiont of host cell wall relationship: part_of GO:0046718 ! viral entry into host cell

[Term] id: GO:0098996 name: disruption of host cell glycocalyx during viral entry namespace: biological_process def: "The disruption of host cell glycocalyx by viral proteins during virus entry" [GOC:dos] synonym: "catabolism of host glycocalyx during viral entry" EXACT [] synonym: "degradation of host capsule during virus entry" EXACT [VZ:3896] synonym: "degradation of host glycocalyx during viral entry" EXACT [] synonym: "disassembly of glycocalyx during viral entry" EXACT [] xref: VZ:3938 is_a: GO:0098933 ! disruption by symbiont of host cell envelope relationship: part_of GO:0046718 ! viral entry into host cell

[Term] id: GO:0098997 name: fusion of virus membrane with host outer membrane namespace: biological_process def: "Fusion of a viral membrane with the host cell outer membrane during viral entry." [GOC:dos, VZ:3941] subset: virus_checked synonym: "fusion of viral membrane with host outer membrane" RELATED [GOC:dos, VZ:3941] synonym: "viral envelope fusion" BROAD [] synonym: "viral envelope fusion with host outer membrane" EXACT [] synonym: "viral penetration via membrane fusion" BROAD [] synonym: "viral-cell fusion molecule activity" RELATED [] xref: VZ:3941 "Fusion of virus membrane with host cell membrane" is_a: GO:0039663 ! membrane fusion involved in viral entry into host cell intersection_of: GO:0061025 ! membrane fusion intersection_of: results_in_fusion_of GO:0019031 ! viral envelope intersection_of: results_in_fusion_of GO:0039662 ! host cell outer membrane

[Term] id: GO:0099000 name: viral genome ejection through host cell envelope, contracile tail mechanism namespace: biological_process def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a contractile tail ejection system consisting of a baseplate, a central tube and an external contractile sheath. Upon binding to the host cell surface, the baseplate changes its conformation and triggers sheath contraction, driving the rigid internal tail tube through the cell envelope." [GOC:dos, PMID:26283379, VZ:3950] synonym: "viral contractile tail ejection system" EXACT [VZ:3950] xref: VZ:3950 is_a: GO:0039678 ! viral genome ejection through host cell envelope is_a: GO:0046794 ! transport of virus

[Term] id: GO:0099001 name: viral genome ejection through host cell envelope, long flexible tail mechanism namespace: biological_process def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a long, flexible tail ejection system consisting a baseplate, a central tube and a terminator complex which attaches the tail to the phage capsid. Upon binding to the host cell surface, the baseplate changes its conformation and triggers genome ejection into the host cell cytoplasm. " [GOC:dos, PMID:22297512, VZ:3952] synonym: "viral long flexible tail ejection system" EXACT [VZ:3952] xref: VZ:3952 is_a: GO:0039678 ! viral genome ejection through host cell envelope is_a: GO:0046794 ! transport of virus

[Term] id: GO:0099002 name: viral genome ejection through host cell envelope, short tail mechanism namespace: biological_process def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a short tail ejection system consisting a central tube, the connector which attaches the tail to the phage capsid and releases inner core proteins. Upon binding to the host cell surface, the phage displays a tube-like extension of its short tail that penetrates both host membranes. This tail extension comes from the release of viral core proteins with channel forming properties." [GOC:dos, PMID:22297513, VZ:3954] synonym: "viral short tail ejection system" EXACT [VZ:3954] xref: VZ:3954 is_a: GO:0039678 ! viral genome ejection through host cell envelope is_a: GO:0046794 ! transport of virus

[Term] id: GO:0099006 name: viral entry via permeabalization of endosomal membrane namespace: biological_process def: "The entry of a non-enveloped virus into a host eukaryotic cell, following endocytosis, via permeabalisation of the endosomal membrane by membrane penetration protein(s) associated with the viral capsid. In some cases, viral membrane-penetration protein require first to be activated to display its membrane penetrating activity. Activation can be due to receptor binding or the acidic pH of the endosomal lumen." [PMID:15329727, VZ:985] synonym: "viral penetration via permeabilization of host membrane" BROAD [vz:985] xref: VZ:985 is_a: GO:0046718 ! viral entry into host cell

[Term] id: GO:0099007 name: extrinsic component of presynaptic endosome membrane namespace: cellular_component def: "The component of the presynaptic endosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:autophagy, GOC:mf] subset: goslim_synapse intersection_of: GO:0019898 ! extrinsic component of membrane intersection_of: part_of GO:0098954 ! presynaptic endosome membrane

[Term] id: GO:0099008 name: viral entry via permeabalization of inner membrane namespace: biological_process def: "The entry of a non-enveloped virus into the cytoplasm of a host prokaryotic cell, following fusion with the outer membrane, via permeabalisation of the plasma (inner) membrane. In the case of some double stranded RNA viruses of prokaryotes this occurs via interaction of a membrane-interacting component of the capsid, leading to depolarization an permeabalization of the plasma membrane." [PMID:15795287, PMID:20427561, VZ:985] synonym: "viral penetration via permeabilization of host membrane" BROAD [vz:985] xref: VZ:985 is_a: GO:0046718 ! viral entry into host cell

[Term] id: GO:0099009 name: viral genome circularization namespace: biological_process def: "The circularization of a viral genome following infection of a host cell. This is common amongst bacterial viruses to protect the viral genome ends from nucleases, to convert the linear genome to an integrative precursor or to give rise to the replicative form of the genome. It can be mediated by covalent closure of the DNA sticky ends, recombinaison between redundant terminal sequences or via the binding of a protein at the viral DNA extremities" [PMID:2011894948, PMID:2015489417, PMID:2019523475, PMID:20319596, VZ:3968] xref: VZ:3968 is_a: GO:0016032 ! viral process

[Term] id: GO:0099015 name: degradation of host chromosome by virus namespace: biological_process def: "The catabolic breakdown of the DNA of a host chromosome by a virus. This occurs during infection of bacteria by some phages. It frees up a large pool of nucleoside 5'-triphophates for use in viral DNA synthesis." [PMID:163355, PMID:335083, PMID:3972821, PMID:5263754, VZ:3947] xref: VZ:3947 is_a: GO:0039637 ! catabolism by virus of host DNA

[Term] id: GO:0099016 name: DNA end degradation evasion by virus namespace: biological_process def: "Any process, either active or passive, by which a virus evades and end degredation of its DNA when free viral-DNA ends are exposed as part of its life-cycle. For example, some bacteriophages encode proteins that bind to free viral DNA ends, protecting them from degredation by host exonuclueases." [GOC:dos, VZ:3963] xref: VZ:3963 is_a: GO:0019049 ! evasion or tolerance of host defenses by virus

[Term] id: GO:0099018 name: restriction-modification system evasion by virus namespace: biological_process def: "Any process, either active or passive, by which a virus evades the DNA restriction modification system of its host. Some viruses encode their own methyltransferase in order to protect their genome from host restriction enzymes. Others directly inhibit restruction enzymes while some use unusual bases in their genome to avoid restriction." [PMID:20348932, PMID:23979432, PMID:24123737, VZ:3966] xref: VZ:3966 is_a: GO:0019049 ! evasion or tolerance of host defenses by virus

[dosumis]

Terms remaining:

• [ ] Bacterial host gene expression shutoff by virus 4496
  • Not sure - do we want host-specific terms?
• [ ] Bacterial host transcription shutoff by virus 4497
  • Add synonym to GO:0039653
• [ ] Evasion of bacteria-mediated translation shutoff by virus 3961
  • Add under GO:0019049, also add a term for the bacterial defense process of shutting off viral transcription
• [x] CRISPR-cas system evasion by virus 3962
  • Add under GO:0019049 - Added: CRISPR-CAS system (general term). New term should refer to this.

• [x] Superinfection exclusion 3971
  • [x] TODO relate: 'GO:0039634 ; killing by virus of host cell during superinfection exclusion' & 'GO:0039639 ; suppression by virus of host cell lysis in response to superinfection'

Note - very general parent class chosen. Suggestions for more specific parent most welcome.

• [x] Inhibition of host DNA replication by virus 3948
  • Add under GO:0019054

• [x] Modulation of host virulence by virus 3965

• [ ] Viral exotoxin 3967 Out of scope?

We now have toxin activity (GO:0090729). We might be able to extend this to exotoxin/endotoxin (requires editor discussion). But we can not add terms differentiated by what type of organism expresses them, so viral exotoxin is out.

• [x] Viral extrusion 3951

• [x] Latency-replication switch 3964

  • relationship to GO:0019046 = ?

[dosumis]

"viral extrusion": "The process whereby a filamentous phage particle is released from a bacterial host cell via a concerted mechanism of assembly and secretion. Neosynthesized virions are coordinately exported as they are assembled at the cell surface in a secretory process that leaves the host cell fully viable. Non-capsid proteins form structures that facilitate translocation through the inner membrane and outer membranes. A viral single-stranded DNA binding protein coats progeny viral DNA molecules to generate the intracellular precursor for assembly of phage particles as they are extruded through the membranes of the bacterial host. The structural proteins of the virus are anchored in the inner membrane before their incorporation into the phage particle. As assembly proceeds, the phage genome traverses the inner and outer membranes until the entire DNA molecule has been coated and extruded." [PMID:2024582831, VZ:3951] xref: VZ:3951 SubClassOf: 'non-lytic viral release'

[SIBvirus]

Hi David, Thanks for the work done so far! Here are my comments, should be in bold ;-) I hope you can understand them. Don't hesitate to tell me if anything is not clear. Cheers, Chantal

[Term] id: GO:0098931 name: virion attachment to host cell flagellum

_"flagellum of a cell surface" sounds a little bit strange... _ _I would rather say: _

def: "The process by which a virion attaches to a the host cell flagellum. Some DNA bacterial viruses use flagella to attach to the host cell. This contact with the flagellum facilitates concentration of phage particles around the entry receptor on the bacterial cell surface. [GOC:dos, VZ:3949] subset: virus_checked

VZ 3949 is not "Pilus-mediated viral adsorption onto host cell" correction:

xref: VZ:3949 "Viral attachment to host cell flagellum " is_a: GO:0019062 ! virion attachment to host cell

[Term] id: GO:0098932 name: disruption by virus of host cell wall petidoglycan during virus entry namespace: biological_process

Why "symbiont" and not "virus" in the definition since the term is focused on viruses? Mention the purpose of this breakdown -> mention viral entry?

def: "A process carried out by a virus that breaks down peptidoglycans in the cell wall of its host during virus entry. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:dos, VZ:3940]

Does "by organism" refer to the virus? I would not add the synonyms containing "organism" since an organism is defined as consisting of one or more cells. The virus is therefore not an organism

remove? synonym: "catabolism of host cell wall peptidoglycan by organism" EXACT [] remove? synonym: "degradation of host cell wall petidoglycan by organism" EXACT [] synonym: "degradation of host peptidoglycans during virus entry" EXACT [VZ:3940] remove? synonym: "disassembly by organism of host cell wall peptidoglycan" EXACT [] synonym: "disassembly by symbiont of host cell wall peptidoglycan" EXACT [] xref: VZ:3940 is_a: GO:0044661 ! disruption by virus of host cell is_a: GO:0052009 ! disruption by symbiont of host cell wall relationship: part_of GO:0046718 ! viral entry into host cell

[Term] id: GO:0098933 name: disruption by symbiont of host cell envelope namespace: biological_process def: "The breakdown of the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684] subset: gosubset_prok

"by another organism" might be clearer?

synonym: "catabolism of host cell wall by organism" EXACT [] synonym: "degradation of host cell wall by organism" EXACT [] synonym: "disassembly by organism of host cell wall" EXACT [] synonym: "disassembly by symbiont of host cell wall" EXACT [] is_a: GO:0052008 ! disruption by symbiont of host cellular component is_a: GO:0052020 ! modification by symbiont of host cell wall is_a: GO:0052339 ! disruption by organism of cell wall of other organism involved in symbiotic interaction

[Term] id: GO:0098994 name: disruption of host cell envelope during viral entry namespace: biological_process

The bacterial cell envelope is defined as the membrane(s) and peptidoglycans (PG) and (sometimes) capsule cf. GO:0030313/cell envelope "...includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present." The definition must thus not be retricted to PG

def: "The disruption of host cell envelope by viral proteins during virus entry. The host cell envelope is a complex multilayered structure that includes the cytoplasmic membrane, the cell wall and, in some cases, an outer membrane, a capsule." [GOC:dos]

synonym: "catabolism of host cell wall during viral entry" EXACT [] synonym: "degradation of host cell envelope components during virus entry" EXACT [VZ:3938] synonym: "degradation of host cell wall during viral entry" EXACT [] synonym: "disassembly of host cell wall during viral entry" EXACT [] xref: VZ:3938 is_a: GO:0098933 ! disruption by symbiont of host cell envelope intersection_of: GO:0098933 ! disruption by symbiont of host cell envelope intersection_of: part_of GO:0046718 ! viral entry into host cell

[Term] id: GO:0098995 name: disruption by virus of host envelope lipopolysaccharide during virus entry namespace: biological_process def: "The breakdown of lipopolysaccharides in a host cell envelope during virus entry into a host cell. For example a phage entering a gram-negative bacterium may actively break down outer membrane lipopolysaccharides." [GOC:dos, VZ:3940] subset: gosubset_prok

Does "by organism" refer to the virus? I would not add the synonyms containing "organism" since an organism is defined as consisting of one or more cells. The virus is therefore not an organism -> remove?synonym: "catabolism of host cell wall peptidoglycan by organism" EXACT [] synonym: "degradation of host cell envelope lipopolysaccharide during viral entry" EXACT [] synonym: "degradation of host lipopolysaccharide during virus entry" EXACT [VZ:394] synonym: "disassembly by virus of outer membrane lipopolysaccharide during viral entry" NARROW [] xref: VZ:3939 is_a: GO:0044661 ! disruption by virus of host cell is_a: GO:0052009 ! disruption by symbiont of host cell wall relationship: part_of GO:0046718 ! viral entry into host cell

[Term] id: GO:0098996 name: disruption of host cell glycocalyx during viral entry namespace: biological_process def: "The disruption of host cell glycocalyx by viral proteins during virus entry" [GOC:dos] synonym: "catabolism of host glycocalyx during viral entry" EXACT [] synonym: "degradation of host capsule during virus entry" EXACT [VZ:3896] synonym: "degradation of host glycocalyx during viral entry" EXACT [] synonym: "disassembly of glycocalyx during viral entry" EXACT [] xref: VZ:3938 add disruption by virus of host cell?: is_a: GO:0044661 ! disruption by virus of host cell is_a: GO:0098933 ! disruption by symbiont of host cell envelope relationship: part_of GO:0046718 ! viral entry into host cell

[Term] id: GO:0098997 name: fusion of virus membrane with host outer membrane namespace: biological_process def: "Fusion of a viral membrane with the host cell outer membrane during viral entry." [GOC:dos, VZ:3941] subset: virus_checked synonym: "fusion of viral membrane with host outer membrane" RELATED [GOC:dos, VZ:3941] synonym: "viral envelope fusion" BROAD [] synonym: "viral envelope fusion with host outer membrane" EXACT [] synonym: "viral penetration via membrane fusion" BROAD [] synonym: "viral-cell fusion molecule activity" RELATED [] xref: VZ:3941 "Fusion of virus membrane with host cell membrane" is_a: GO:0039663 ! membrane fusion involved in viral entry into host cell intersection_of: GO:0061025 ! membrane fusion intersection_of: results_in_fusion_of GO:0019031 ! viral envelope intersection_of: results_in_fusion_of GO:0039662 ! host cell outer membrane

[Term] id: GO:0099000 name: viral genome ejection through host cell envelope, contracile tail mechanism

I have classified this term as a "Cellular component". Do you think I should change it for "biological_process"? I use the term "Viral contractile tail ejection system" to tag all the proteins that compose this type of ejection system

?namespace: biological_process def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a contractile tail ejection system consisting of a baseplate, a central tube and an external contractile sheath. Upon binding to the host cell surface, the baseplate changes its conformation and triggers sheath contraction, driving the rigid internal tail tube through the cell envelope." [GOC:dos, PMID:26283379, VZ:3950] synonym: "viral contractile tail ejection system" EXACT [VZ:3950] xref: VZ:3950 is_a: GO:0039678 ! viral genome ejection through host cell envelope

Transport of virus?? Only the genome is ejected... Why not relate it to viral entry? -> relationship: part_of GO:0046718 ! viral entry into host cell add?is_a: GO:0039678 ! viral genome ejection through host cell envelope remove?is_a: GO:0046794 ! transport of virus

[Term] id: GO:0099001 name: viral genome ejection through host cell envelope, long flexible tail mechanism

I have classified this term as a "Cellular component". Do you think I should change it for "biological_process"? I use the term "viral long flexible tail ejection system" to tag all the proteins that compose this type of ejection system...

namespace: biological_process def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a long, flexible tail ejection system consisting a baseplate, a central tube and a terminator complex which attaches the tail to the phage capsid. Upon binding to the host cell surface, the baseplate changes its conformation and triggers genome ejection into the host cell cytoplasm. " [GOC:dos, PMID:22297512, VZ:3952] synonym: "viral long flexible tail ejection system" EXACT [VZ:3952] xref: VZ:3952 -> idem above relationship: part_of GO:0046718 ! viral entry into host cell add?is_a: GO:0039678 ! viral genome ejection through host cell envelope remove?is_a: GO:0046794 ! transport of virus

[Term] id: GO:0099002 name: viral genome ejection through host cell envelope, short tail mechanism

I have classified this term as a "Cellular component". Do you think I should change it for "biological_process"? I use the term "Viral short tail ejection system" to tag all the proteins that compose this type of ejection system...

namespace: biological_process def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a short tail ejection system consisting a central tube, the connector which attaches the tail to the phage capsid and releases inner core proteins. Upon binding to the host cell surface, the phage displays a tube-like extension of its short tail that penetrates both host membranes. This tail extension comes from the release of viral core proteins with channel forming properties." [GOC:dos, PMID:22297513, VZ:3954] synonym: "viral short tail ejection system" EXACT [VZ:3954] xref: VZ:3954 -> idem above relationship: part_of GO:0046718 ! viral entry into host cell add?is_a: GO:0039678 ! viral genome ejection through host cell envelope remove?is_a: GO:0046794 ! transport of virus

[Term] id: GO:0099006

**?Concept already exists? cf. GO:0075502 "endosome membrane permeabilization involved in viral entry into host cell" -> Just seems to be equivalent...

Maybe just rename GO:0075502 as "viral entry via permeabilization of host membrane" and adapt the definition with the one below?

GO:0099006 could be changed for "viral entry via permeabilization of host membrane"? This term could then be used as a term above both "endosome membrane permeabilization involved in viral entry into host cell" and "viral entry via permeabilization of inner membrane"? It would then fit to VZ def. (=permeabilization of endosome membrane OR plasma membrane (prokaryotic dsRNA viruses)

"permeabilization"**

name: viral entry via permeabilization of endosomal membrane namespace: biological_process

"permeabilization", "requires"

def: "The entry of a non-enveloped virus into a host eukaryotic cell, following endocytosis, via permeabilization of the endosomal membrane by membrane penetration protein(s) associated with the viral capsid. In some cases, viral membrane-penetration protein requires first to be activated to display its membrane penetrating activity. Activation can be due to receptor binding or the acidic pH of the endosomal lumen." [PMID:15329727, VZ:985] synonym: "viral penetration via permeabilization of host membrane" BROAD [vz:985] xref: VZ:985 is_a: GO:0046718 ! viral entry into host cell

[Term] id: GO:0099007 name: extrinsic component of presynaptic endosome membrane namespace: cellular_component def: "The component of the presynaptic endosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:autophagy, GOC:mf] subset: goslim_synapse intersection_of: GO:0019898 ! extrinsic component of membrane intersection_of: part_of GO:0098954 ! presynaptic endosome membrane

[Term] id: GO:0099008

"permeabilization" _add "host" _

name: viral entry via permeabilization of host inner membrane namespace: biological_process def: "The entry of a non-enveloped virus into the cytoplasm of a host prokaryotic cell, following fusion with the outer membrane, via permeabalisation of the plasma (inner) membrane. In the case of some double stranded RNA viruses of prokaryotes this occurs via interaction of a membrane-interacting component of the capsid, leading to depolarization an permeabilization of the plasma membrane." [PMID:15795287, PMID:20427561, VZ:985] synonym: "viral penetration via permeabilization of host membrane" BROAD [vz:985] xref: VZ:985 is_a: GO:0046718 ! viral entry into host cell

[Term] id: GO:0099009 name: viral genome circularization namespace: biological_process def: "The circularization of a viral genome following infection of a host cell. This is common amongst bacterial viruses to protect the viral genome ends from nucleases, to convert the linear genome to an integrative precursor or to give rise to the replicative form of the genome. It can be mediated by covalent closure of the DNA sticky ends, recombinaison between redundant terminal sequences or via the binding of a protein at the viral DNA extremities" [PMID:2011894948, PMID:2015489417, PMID:2019523475, PMID:20319596, VZ:3968] xref: VZ:3968 is_a: GO:0016032 ! viral process

[Term] id: GO:0099015 name: degradation of host chromosome by virus namespace: biological_process def: "The catabolic breakdown of the DNA of a host chromosome by a virus. This occurs during infection of bacteria by some phages. It frees up a large pool of nucleoside 5'-triphophates for use in viral DNA synthesis." [PMID:163355, PMID:335083, PMID:3972821, PMID:5263754, VZ:3947] xref: VZ:3947 is_a: GO:0039637 ! catabolism by virus of host DNA

[Term] id: GO:0099016 name: DNA end degradation evasion by virus namespace: biological_process

degradation ends exonucleases

def: "Any process, either active or passive, by which a virus evades and ends degradation of its DNA when free viral-DNA ends are exposed as part of its life-cycle. For example, some bacteriophages encode proteins that bind to free viral DNA ends, protecting them from degradation by host exonucleases." [GOC:dos, VZ:3963] xref: VZ:3963 is_a: GO:0019049 ! evasion or tolerance of host defenses by virus

[Term] id: GO:0099018 name: restriction-modification system evasion by virus namespace: biological_process def: "Any process, either active or passive, by which a virus evades the DNA restriction modification system of its host. Some viruses encode their own methyltransferase in order to protect their genome from host restriction enzymes. Others directly inhibit restruction enzymes while some use unusual bases in their genome to avoid restriction." [PMID:20348932, PMID:23979432, PMID:24123737, VZ:3966] xref: VZ:3966 is_a: GO:0019049 ! evasion or tolerance of host defenses by virus

[SIBvirus]

Just one typo: "t" is missing in "contracile" cf. id: GO:0099000 name: viral genome ejection through host cell envelope, contracile tail mechanism

[dosumis]

name: virion attachment to host cell flagellum

def: "The process by which a virion attaches to a the host cell flagellum. Some DNA bacterial viruses use flagella to attach to the host cell. This contact with the flagellum facilitates concentration of phage particles around the entry receptor on the bacterial cell surface. [GOC:dos, VZ:3949]

Fixed

VZ 3949 is not "Pilus-mediated viral adsorption onto host cell" correction:

xref: VZ:3949 "Viral attachment to host cell flagellum " is_a: GO:0019062 ! virion attachment to host cell

Fixed

[Term] id: GO:0098932 name: disruption by virus of host cell wall petidoglycan during virus entry

Why "symbiont" and not "virus" in the definition since the term is focused on viruses? Mention the purpose of this breakdown -> mention viral entry?

def: "A process carried out by a virus that breaks down peptidoglycans in the cell wall of its host during virus entry. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:dos, VZ:3940]

Fixed. Including removal of synonym.

name: disruption by symbiont of host cell envelope namespace: biological_process def: "The breakdown of the host cell wall. The host is defined as the larger of the organisms > involved in a symbiotic interaction." [ISBN:0198547684]

[Term] id: GO:0098994 name: disruption of host cell envelope during viral entry

Definition simplified: def: "The process by which a symbiont breaks down the cell wall of its host. The host is defined as the larger of the organisms involved in a symbiotic interaction."

disruption by virus of host envelope lipopolysaccharide during virus entry

Removed offending synonyms

name: viral genome ejection through host cell envelope, contracile tail mechanism

Corrected typo in name

name: viral genome ejection through host cell envelope, contracile tail mechanism name: viral genome ejection through host cell envelope, short tail mechanism viral genome ejection through host cell envelope, long flexible tail mechanism

I have classified this term as a "Cellular component". Do you think I should change it for "biological_process"? I use the term "Viral contractile tail ejection system" to tag all the proteins that compose this type of ejection system

I can add cellular component terms in addition to the BP terms and link the two via a capable_of (or capable_of_part_of) link. Would that work for you?

Transport of virus?? Only the genome is ejected... Why not relate it to viral entry? -> relationship: part_of GO:0046718 ! viral entry into host cell add?is_a: GO:0039678 ! viral genome ejection through host cell envelope remove?is_a: GO:0046794 ! transport of virus

I have removed is_a GO:0046794 ! transport of virus from these leaf nodes and the parent class. I have kept the relationship on the parent class as is_a 'viral entry into host cell' rather than 'part of' changing would leave this without an is_a parent. Could potentially reconsider this if we can find a more suitable home.

GO:0075502 viral entry via permeabalization of endosomal membrane **?Concept already exists? cf. GO:0075502 "endosome membrane permeabilization involved in viral entry into host cell" -> Just seems to be equivalent...

They're certainly very close. Former could potentially include additional steps other than permeabilization, but this is probably too subtle to worry about.

• [ ] TODO merge GO:0075502 & GO:0075502. Which term you think should win?

name: DNA end degradation evasion by virus

Fixed typos.

[SIBvirus]

Hi David, Many thanks for the corrections! Here are my answers to your questions and some modifications left that should be done, I think. I let you see if you agree with these last points! Cheers, Chantal

1. [Term] id: GO:0098994 name: disruption of host cell envelope during viral entry

remove synonym: "catabolism of host cell wall during viral entry" EXACT synonym: "degradation of host cell envelope components during virus entry" EXACT [VZ:3938] remove synonym: "degradation of host cell wall during viral entry" EXACT remove synonym: "disassembly of host cell wall during viral entry" EXACT

-> these terms are already used as exact synonym of "disruption by virus of host cell wall peptidoglycan during virus entry". They should not be used here I think (envelope is not restricted to the PG)

2. [Term] id: GO:0098932 name: disruption by virus of host cell wall petidoglycan during virus entry

-> Typo: "petidoglycan" should be "peptidoglycan"

3. [Term] id: GO:0098995 name: disruption by virus of host envelope lipopolysaccharide during virus entry

-> lipopolysaccharide is not a PG remove synonym: "catabolism of host cell wall peptidoglycan by organism" EXACT []

4. name: viral genome ejection through host cell envelope, contractile tail mechanism name: viral genome ejection through host cell envelope, short tail mechanism name: viral genome ejection through host cell envelope, long flexible tail mechanism

I can add cellular component terms in addition to the BP terms and link the two via a capable_of (or capable_of_part_of) link. Would that work for you? I have removed is_a GO:0046794 ! transport of virus from these leaf nodes and the parent class. I have kept the relationship on the parent class as is_a 'viral entry into host cell' rather than 'part of' changing would leave this without an is_a parent. Could potentially reconsider this if we can find a more suitable home.

-> That's perfect thanks!

5. id: GO:0099000 -> Typo: "contracile" should be "contractile"

6. TODO merge GO:0075502 & GO:0075502. Which term you think should win?

-> I think you mean GO:0099006 & GO:0075502?

-> I would keep GO:0099006, but could you please fix the typos : "permeabilization" (cf. permeabalization/permeabalisation) and "requires" instead of "require"

-> If possible, I would just rename GO:0075502 as "viral entry via permeabilization of host membrane" and adapt the definition accordingly. GO:0075502 could than be used as a parent term of "viral entry via permeabilization of endosomal membrane" and "viral entry via permeabilization of host inner membrane" which would be very good to have!! GO:0075502 would then fit to VZ 985 (=permeabilization of endosome membrane OR plasma membrane (prokaryotic dsRNA viruses): http://viralzone.expasy.org/all_by_protein/985.html

8.

[Term] id: GO:0099008

-> Could you please fix the typos : "permeabilization" (cf. permeabalization/permeabalisation) and add "host" to the name: -> viral entry via permeabilization of host inner membrane

[SIBvirus]

Hi David, We are invited to write a paper by the end of February in a special issue of Viruses about the work done on the phage ontology/ViralZone. I had a look at what is left to do in the list of phage GO terms and I have a few questions:

-Did you have time to make the last correction I sent Nov. 23?

-Some terms have not been added yet, could you please tell me which of those you might consider to create GO terms from? If some of them are not suitable to be introduced into GO, could you tell me please?

1. [x] Viral receptor tropism switching
2. [ ] Evasion of bacteria-mediated translation shutoff by virus
3. [x] CRISPR-cas system evasion by virus
4. [x] Superinfection exclusion
5. [ ] Inhibition of host DNA replication by virus
6. [x] Modulation of host virulence by virus
7. [ ] Viral exotoxin # Out of scope.
8. [x] Viral attachment to host adhesion receptor
9. [x] Viral attachment to host entry receptor Regarding the last two terms, GO:0098001 and GO:0098002 are almost equivalent, but they are restricted to phages. We need a more general term, because the two step attachment mediated by an attachment receptor followed by the attachment to an entry receptor is a mechanism that is also used by eukaryotic viruses.

Many thanks in advance and a happy new year! Chantal

[dosumis]

Hi Chantal,

Corrections sent on 23rd are all done except merge. I have a grant deadline on Friday so won't get to the rest of your questions this week. I'll work on this again next Monday.

Cheers, David

[SIBvirus]

Hi David, Thanks for the corrections! Do not hesitate to ask if you have any questions on the nine terms left! Cheers, Chantal

[dosumis]

• [x] Viral attachment to host adhesion receptor 3943
• [x] Viral attachment to host entry receptor 3942

[dosumis]

New (not in spreadsheet)

• [x] Viral receptor tropism switching 4498

[dosumis]

Hi Chantal,

I'm working my way through the list of remaining terms. Nearly done. See https://github.com/geneontology/go-ontology/issues/11426#issuecomment-230303760

One quick question: is this mapping correct?

Virion maturation (cf UniProt= only maturation post release) 1946 = GO:0019075 virus maturation

Cheers, David

[SIBvirus]

Hi David,

No, this mapping is not correct because GO:0019075 covers the maturation events that occur inside the host cell or after release. Our UniProt keyword (as well as ViralZone page) only takes into account the maturation events post-release.

Cheers, Chantal

[dosumis]

OK Thanks. I'll make the new term a part of GO:0019075 then.

[SIBvirus]

Great! Thanks, Chantal

[dosumis]

Quick question: Is this mapping correct?

'Latency-replication switch VZ:3964' = 'release from viral latency' GO:0019046

[dosumis]

[SIBvirus]

Hi David,

Regarding your question: Is this mapping correct?

'Latency-replication switch VZ:3964' = 'release from viral latency' GO:0019046

No, this is not correct. The latency-replication switch occurs early after infection and "decides" (probably depending on the presence of certain host proteins related to the physiological state of the bacteria) of the outcome of the infection: either entering latency or replicative infection.

The Go term "release from viral latency" is one step ahead. Latency has already been "chosen" and established. This term describes the end of latency and reactivation of the virus that results in productive replication.

I hope this helps, cheers, Chantal

[SIBvirus]

I have just come across a very interesting paper on this topic! https://www.ncbi.nlm.nih.gov/pubmed/28099413

[SIBvirus]

Hi David,

I had a deeper look at the question about 'Latency-replication switch' (VZ:3964) and your existing term 'release from viral latency' (GO:0019046).

I asked an expert whether we should have one or two GO terms to describe these events. Here is his answer: "I believe that the decision to integrate into the genome and enter a dormancy cycle is separate from the decision to exit the dormancy cycle. Sometimes, however, some genes would be involved in executing both decisions. It is therefore a tough call whether to make it a single Go term or to split the GO terms… I would actually go for a single GO term…"

If these are separate processes, I think they should get two distinct GO terms? Moreover, we cannot be sure that the same proteins are systematically involved in both mechanisms (the lysis-lysogeny decision has been studied in procaryotic viruses and the release from viral latency mostly in eukaryotic viruses...). If a protein is clearly involved in both mechanisms, it will get both GO terms. What do you think?

Another tricky thing is that the term 'Latency-replication switch' is used in the literature for the exit of latency (mostly for herpesviruses) ie for the release from viral latency... It may thus be better to name the decision that has to be made at the onset of infection 'Latency-replication decision' to avoid any confusion (lysis-lysogeny decision has been used in literature, but would be restricted to phages).

So I would propose two terms:

1. latency-replication decision (to be created, VZ:3964, synonyms: lysis-lysogeny decision, lysis-lysogeny switch)

2. release from viral latency (GO:0019046, already OK)

If you agree with all this, I will create a keyword corresponding to ' release from viral latency' in Swiss-Prot as well, so we will be able to add it to the SP2GO mapping.

Regarding SP2GO mapping, I would link (was wrong in the excel file I gave to you): Viral genome integration (KW-1179)->viral genome integration into host DNA (GO:0044826)

Cheers, Chantal

[dosumis]

Hi Chantal, Many thanks for all the detailed info on this. From a quick skim through your plan, I agree it looks like the right approach. I plan to implement next week. Cheers, David

[SIBvirus]

OK! I will create a keyword that can be linked to 'release from viral latency '. I already have a list of proteins that are involved in this mechanism. Thanks, Chantal

[SIBvirus]

Hi David,

Just to let you know that I have create the keyword KW-1252 "Latency-replication decision" that is not released yet but that you may be able to read on our internal site (http://sp.isb-sib.ch/keywords/KW-1252). Can you please tell me when you have integrated the corresponding GO term? The phage list of terms will then be completed :-)!

Regarding SP2GO, I will send you an updated version of my excel file where you have now the new GO terms listed. I have rechecked all the KW-GO pairs, can you confirm me that this corresponds to what is (will be) listed in SP2GO? Or tell me where I can find an updated version of the SP2GO file (so I can check myself)?

Thanks! Cheers, Chantal

[dosumis]

Diff showing edits is here:

https://github.com/geneontology/go-ontology/commit/a86cc6a5e1a107e1b9db9b12224b176483c15cb1

I've modified the def and synonyms on 'release from viral latency' to disentangle it from the decision/switch term.