Changes to GO:0039580 suppression by virus of host PKR activity

[pgaudet]

Hi @pmasson55

GO:0039580 suppression by virus of host PKR activity is mapped to ~KW-1223~  https://www.uniprot.org/keywords/1102 and https://viralzone.expasy.org/554

Looks like proteins annotated to that term inhibit PKR, which is a kinase that regulates eukaryotic translation initiation factor 2.

So - a mapping to 'GO:0039611 suppression by virus of host translation initiation factor activity' + GO:0030291 protein serine/threonine kinase inhibitor activity seems more appropriate, what do you think?

Also - I think this is a type of suppression of innate immune response, also because it is mediated by interferon?

Thanks, Pascale

[pmasson55]

Hi PAscale,

Yes we can do that. Yes it belongs to the inhibition of innate immune response by pathogens for sure... Regards Patrick.

[pgaudet]

Will you redo the mappings in ViralZone?

And I think @pgarmiri and/or @Antonialock do the KW mappings - right ?

Thanks, Pascale

[pgaudet]

Discussing this on the multiorg call - actually the virus is suppressing the host translation suppression program that occurs upon viral infection.

[pgaudet]

Changed term label and definition

id: GO:0039580

• old name: suppression by virus of host PKR activity

• new name: suppression by virus of host PKR signaling

• old def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (protein kinase regulated by RNA) activity. Activation of PKR involves dsRNA binding followed by autophosphorylation. Phosphorylated PKR can then phosphorylate downstream targets such as the translation initiation factor eIF2 to inhibit protein synthesis. Viruses encode a number of mechanisms to inhibit the host antiviral response via PKR, including direct interaction with PKR, promoting degradation of PKR or altering the subcellular location of PKR." [PMID:15207627, UniProtKB-KW:KW-1102, VZ:554]

• new def : "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (Protein Kinase regulated by RNA) signaling. Host PKR signaling includes targets such as the translation initiation factor eIF2alpha, inhibiting protein synthesis as an antiviral response." [PMID:15207627]

[Antonialock]

is that the correct keyword ID?

KW-1223 is mapped to suppression by virus of host TBK1 activity GO:0039723 https://www.uniprot.org/keywords/KW-1223

[pgaudet]

Thanks @Antonialock

The correct KW is https://www.uniprot.org/keywords/1102

[Antonialock]

I mapped kw-1102 to GO:0039611 & GO:0030291 and removed the mapping to GO:0039580

is this what was required here?

[pgaudet]

@Antonialock Actually I dont think mappings should have been changed.

• [x] 'GO:0039611 suppression by virus of host translation initiation factor activity' is not correct - the viral protein inhibits the inhibitor of the translation initiation factor - ie it is one step before. - please remove this

• [x] please add back GO:0039580 suppression by virus of host PKR activity (now named 'suppression by virus of host PKR signaling')

• GO:0030291 protein serine/threonine kinase inhibitor activity is OK

Sorry about the confusion!

Thanks, Pascale

[Antonialock]

ok! done.