ntrs: 3'-5' and 5'-3' pathways of mRNA degradation

[gocentral]

Hi,

I'm curating this paper:

Lotan R, Goler-Baron V, Duek L, Haimovich G, Choder M (2007) The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol 178(7):1133-43 PMID:17875743

They indicate that RPB7 is specifically involved in the 3' to 5' pathway of mRNA degradation. Currently, the most specific process term available is "mRNA catabolic process, exonucleolytic" (GO:291). I remember that the reason that the more specific (5'->3' and 3'->5' terms were not added originally had to due with the rationale that the specific 5'->3' and 3'->5 exo activities are represented in function. However, it seems that RPB7 is involved specifically in the 5'->3' decay pathway without being an exonuclease, so I think the more specific process terms are warranted.

-Karen

Reported by: krchristie

Original Ticket: "geneontology/ontology-requests/4921":https://sourceforge.net/p/geneontology/ontology-requests/4921

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I've made up some defs based on the parent; if they look OK I'd be happy to add the terms:

id: GO:new1 name: mRNA catabolic process, exonucleolytic, 3'-5' def: "The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the ends are not protected by the 5'-cap or the 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction." [GOC:krc, GOC:mah] is_a: GO:0000291 ! mRNA catabolic process, exonucleolytic

id: GO:new2 name: mRNA catabolic process, exonucleolytic, 5'-3' def: "The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the ends are not protected by the 5'-cap or the 3'-poly(A) tail; degradation proceeds in the 5' to 3' direction." [GOC:krc, GOC:mah] is_a: GO:0000291 ! mRNA catabolic process, exonucleolytic

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Original comment by: mah11

[gocentral]

Logged In: YES user_id=473890 Originator: YES

I think that for both, the first sentence needs to be modified with respect to what the RNA is not protected by. For the 3'-5' pathway, the 5' cap is irrelevant, and similarly for the 5'-3' pathway, the poly(A) tail is irrelevant. So, maybe we could rephrase like this:

id: GO:new1 name: mRNA catabolic process, exonucleolytic, 3'-5' def: "The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 3' end is not protected by the a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction." [GOC:krc, GOC:mah] is_a: GO:0000291 ! mRNA catabolic process, exonucleolytic

id: GO:new2 name: mRNA catabolic process, exonucleolytic, 5'-3' def: "The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 5' end is not protected by a 5'-cap; degradation proceeds in the 5' to 3' direction." [GOC:krc, GOC:mah] is_a: GO:0000291 ! mRNA catabolic process, exonucleolytic

If those defs look OK to you, please feel free to add them the next time you're editing.

thanks,

-K

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Terms added, with cumbersome names consistent with recent changes, and defs from the latest comment here:

nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' GO:0034427 nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' GO:0034428

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11