function term for obsoletion GO:0030363

[gocentral]

pre-mRNA cleavage factor activity

looks like a process term

see def 'Any activity required for the process of mRNA cleavage'

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/1166":https://sourceforge.net/p/geneontology/ontology-requests/1166

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Agree - that term, plus its children (cleavage stimulation factor activity ; GO:0030365, cleavage/polyadenylation specificity factor activity ; GO:0030364) and a sibling (pre-mRNA splicing factor activity ; GO:0008248) all look like gene products with "activity" stuck on the end to me.

Original comment by: girlwithglasses

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GO:0008248 is a parent of three binding activities, so in theory it could be renamed as a binding term. But there are probably annotations to all sorts of other thing, so I'll send out a message.

Would it be useful to have a grouping term for the terms that are now children of GO:0008248? i.e. pre-mRNA 3'-splice site binding ; GO:0030628 pre-mRNA 5'-splice site binding ; GO:0030627 pre-mRNA branch point binding ; GO:0045131

Original comment by: mah11

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proposal-to-obsolete message sent ... here's a copy.

Proposal to obsolete three function ontology terms that impact existing annotation

The proposal has been made to obsolete

pre-mRNA splicing factor activity ; GO:0008248 [549] pre-mRNA cleavage factor activity ; GO:0030363 [6] cleavage and polyadenylylation specificity factor activity ; GO:0030364 [58] cleavage stimulation factor activity ; GO:0030365 [0]

There exist today annotations to these terms as follows (not including IEA annotations):

pre-mRNA splicing factor activity ; GO:0008248 GeneDB_Pfalciparum 23 GeneDB_Tbrucei 6 FB 152 MGI 27 RGD 3 SGD 48 TAIR 12 TIGR_Ath1 47 UniProt 231 (Note that these are annotations directly to GO:0008248; the child terms will be retained, so annotations to them are unaffected.)

pre-mRNA cleavage factor activity ; GO:0030363 SGD 3 UniProt 3

cleavage and polyadenylylation specificity factor activity ; GO:0030364 GeneDB_Spombe 1 SGD 19 TAIR 2 TIGR_Ath1 2 UniProt 14

These terms are not used in any GO slim set maintained within the OBO flat file.

Terms used in external mappings: cleavage/polyadenylation specificity factor activity ; GO:0030364 reactome2go: Reactome:72218 > GO:cleavage/polyadenylation specificity factor activity ; GO:0030364

pre-mRNA splicing factor activity ; GO:0008248 interpro2go: InterPro:IPR001163 Small nuclear ribonucleoprotein (Sm protein) > GO:pre-mRNA splicing factor activity ; GO:0008248 interpro2go: InterPro:IPR004098 Prp18 > GO:pre-mRNA splicing factor activity ; GO:0008248 pfam2go: Pfam:PF01423 LSM > GO:pre-mRNA splicing factor activity ; GO:0008248 pfam2go: Pfam:PF02840 Prp18 > GO:pre-mRNA splicing factor activity ; GO:0008248 smart2go: SMART:SM00651 Sm > GO:pre-mRNA splicing factor activity ; GO:0008248 tigrfams2go: TIGR_TIGRFAMS:TIGR01622 splicing factor, CC1-like family > GO:pre-mRNA splicing factor activity ; GO:0008248

The reason for this proposal is that GO:0008248 and GO:0030363 represent process information, and GO:0030364 and GO:0030365 are protein complex names with the word 'activity' attached.

Suggested terms to use to replace annotations: pre-mRNA splicing factor activity ; GO:0008248 process RNA splicing ; GO:0008380 (or children)

pre-mRNA cleavage factor activity ; GO:0030363 process mRNA cleavage GO:006379 (I will define it based on PMID 10357856)

cleavage and polyadenylylation specificity factor activity ; GO:0030364 component mRNA cleavage and polyadenylation specificity factor complex ; GO:005847 process mRNA polyadenylylation ; GO:0006378 or mRNA cleavage GO: 006379

cleavage stimulation factor activity ; GO:0030365 component mRNA cleavage stimulating factor complex ; GO:0005848 process mRNA cleavage GO:006379

Link to SourceForge discussion: http://sourceforge.net/tracker/index.php? func=detail&aid=818610&group_id=36855&atid=440764

The two-week comment period ends on Monday, January 24, 2005.

m

Original comment by: mah11

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I think tweaking the defs or replacing the term with a new activity term would be better. It appears, for example, GO:0008248, is used to group three specific binding activities. In the absence of data to know which of these three a protein is binding, a better
and call it "pre-mRNA splice-site binding"

GO:0030363 pre-mRNA cleavage factor activity GO:0030364 cleavage and polyadenylylation specificity factor activity GO:0030365 cleavage stimulation factor activity By their definitions, they of course all would have a parent of pre-mRNA binding. However, they appear to not have any other "molecular" function (stimulation, and directing specificity are definitely assayable, but we don't know HOW they act at the molecular level other than we know that they first bind the pre-mRNA). In each case they appear to be enhancing or directing a (separate?) cleavage (endonuclease) activity.

Original comment by: hdrabkin

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I'd be happy to rename GO:0008248 instead of making it obsolete, as long as all of the annotations to it are still correct. I'll ask on the list.

m

Original comment by: mah11

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It looks rather as though we ought to make GO:0008248 obsolete. Relevant thread from the mailing list:

---------- Forwarded message ---------- Date: Tue, 11 Jan 2005 10:49:01 -0500 From: Harold Drabkin <hjd@informatics.jax.org> To: Midori Harris <midori@ebi.ac.uk>, Karen Christie <kchris@genome.stanford.edu> Cc: Maria Costanzo <maria@genome.stanford.edu>, go@genome.stanford.edu Subject: Re: Alert: Proposal to obsolete three function ontology terms that impact existing annotation

I think I have to agree. I've just finished looking at a few of ours. It's not always clear that specific RNA binding is being shown in the references I've quickly looked at. So, the migration may be a problem.

On 1/11/05 9:42 AM, "Midori Harris" <midori@ebi.ac.uk> wrote:

> That was my concern as well, but I thought it wouldn't hurt to have > a look at the gene products. > > If renaming is too risky, we can add 'pre-mRNA splice site binding' as > a > new term, and suggest it for updates. > > m > > On Tue, 11 Jan 2005, Karen Christie wrote: > >> Hi, >> >> I'm not sure that changing 8248 to "pre-mRNA splice site binding" is >> going >> to work. Just taking a quick look at the things currently annotated to >> this term in SGD, I notice that it includes the LSM genes. These are a >> group of genes (7-8 I think) that form a structural component of most >> of >> the spliceosomal snRNPs. These proteins interact with the snRNAs, >> e.g. U1, >> U2, etc., so clearly are RNA binding but their substrate for >> interaction >> is a portion of the snRNA, not the mRNA splice sites. With my current >> understanding of splicing, I don't think it would be safe to say that >> the >> majority of things currently annotated to 8248 could be correctly >> annotated to a term narrowed to mean 'pre-mRNA splice site binding'. >> >> Just a quick comment before I try to get back to sleep. I can >> participate >> more in this discussion, if needed, later in the day. >> >> -Karen >> >> >> On Tue, 11 Jan 2005, Maria Costanzo wrote: >> >>> Hi Midori, >>> >>> This sounds like a reasonable alternative to obsoletion for >>> GO:0008248. >>> Since it's a child of 'RNA binding', it's a good bet that the gene >>> products annotated to it bind to splice sites (we'll check to make >>> sure, of course). I think it would be useful to make this a generic >>> 'splice site binding' term since it has child terms describing >>> binding >>> to specific splice sites. >>> >>> Maria >>> >>> On Jan 11, 2005, at 8:02 AM, Midori Harris wrote: >>> >>>> An alternative for GO:0008248 might be to rename it: >>>> >>>> new name: pre-mRNA splice site binding >>>> new def: interacting selectively with any of the splicing >>>> recognition >>>> sites in a pre-mRNA molecule >>>> >>>> This would work if the new definition applies to all gene products >>>> annotated to this term. So if the groups using GO:0008248 could >>>> look at >>>> their annotations and mappings (list included below), this term can >>>> be >>>> saved from obsolescence. >>>> >>>> midori

Original comment by: mah11

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Hi,

Regarding, GO:0008248, I think we should have a term for this type of RNA splicing activity. I think this would be consistent with the fact that the function ontology contains terms for things like "translation factor activity" and "transcription factor activity". However, I think it would need a name change, some refinement of the definition, and to be moved. I think this term should encompass the activity of both the spliceosomal proteins and also the proteins that assist splicing of Group I, II, or III introns in organelles such as mitochondria.

It may be possible to maintain the same GOid, depending on what's currently annotated. The only things that I see that look obviously incorrect for the new def are a couple for U7 proteins, but I don't think U7 proteins should have been annotated to the old def of this term either. U7 is involved in 3'-end formation of histone mRNAs, not in intron removal.

---Lsm10 MGI ISS U7 snRNP-specific Sm-like protein LSM10 ---Lsm11 MGI ISS U7 snRNP-specific Sm-like protein LSM11

However, there are a lot of things I don't recognize. It might be safer to obsolete this ID and replace it with a new term, but perhaps other affected groups could scan through theirs and see what they think.

Proposal for changed term:

1. change name to not be specific to mRNA, since these introns occur in non-mRNA. Sorry about the ugly name, but with the loss of the "m", there needs to be a way to indicate that this term is not appropriate for the gene products which mediate splicing of tRNAs, which does not occur by the same mechanism.

2. change parentage to be under "RNA binding" instead of "mRNA binding"

3. The current three children of this term should stay under "mRNA binding", and I think also have parentage under "RNA splicing activity, transesterification mechanism"

4. I don't, at the moment, think that there is any need to have a new child term of the newly positioned 8248 (below 8248 and above the current three children of 8248), specifically for the proteins involved in spliceosomal splicing, because I think the def I'm proposing is sufficient for those as well as the solitary proteins which assist Group I, II, and III intron splicing in the mitochondrion and other organelles.

current def: name: pre-mRNA splicing factor activity namespace: molecular_function def: "An activity involved in the removal of an intron from a pre-mRNA." [GO:jl]

new: name: RNA splicing factor activity, transesterification mechanism def: An activity which binds RNA and functions to assist splicing of substrate RNA(s) by facilitating the formation and stabilization of a catalytic conformation in which the splice junctions of the RNA(s) to be spliced are positioned for a transesterification reaction that occurs between two sites within the RNA(s) to be spliced.

comment: Nuclear mRNA, Group I, Group II, and Group III introns are all spliced by a series of two transesterification reactions that occur within the RNA itself, or between two RNAs in trans splicing. Some of these require one or more proteins to stabilize the catalytic conformation, while others are autocatalytic. Note that tRNA introns are spliced by a different catalytic mechanism. (not necessarily in appropriate format for a comment yet)

current:

-%RNA binding ; GO:0003723 --%mRNA binding ; GO:0003729 ---%pre-mRNA splicing factor activity ; GO:0008248 ----%pre-mRNA 3'-splice site binding ; GO:0030628 ----%pre-mRNA 5'-splice site binding ; GO:0030607 ----%pre-mRNA branch point binding ; GO:0045131

new:

-%RNA binding ; GO:0003723 --%RNA splicing factor activity, tranesterification mechanism;GO:0008248 ---%pre-mRNA 3'-splice site binding ; GO:0030628 ---%pre-mRNA 5'-splice site binding ; GO:0030607 ---%pre-mRNA branch point binding ; GO:0045131 --%mRNA binding ; GO:0003729 ---%pre-mRNA 3'-splice site binding ; GO:0030628 ---%pre-mRNA 5'-splice site binding ; GO:0030607 ---%pre-mRNA branch point binding ; GO:0045131

Original comment by: krchristie

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Hi,

I'd like to request an extension of one week, until February 14th, to investigate these three terms:

pre-mRNA cleavage factor activity ; GO:0030363 [6] cleavage and polyadenylylation specificity factor activity ; GO:0030364 [58] cleavage stimulation factor activity ; GO:0030365 [0]

The literature on these is generally completely unconnected to that of the 4th term that was in this proposal, GO:0008248, and I just don't feel I understand the situation for these three terms yet. I think it would be better to look into it further than to obsolete terms hastily and then realize I actually do need function terms, though I agree that the current definitions are not appropriate, so if there are functions to be represented here that new defs would be needed to describe any actual functions.

thanks,

-Karen

Original comment by: krchristie

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For GO:0008248, the new name, definition, and position are fine with me. Whether to keep the old ID or obsolete- and-issue-new-ID comes down to the existing annotation. I'll try to prod the list again; if all groups that have annotations (esecially non-IEA) check theirs and assure us that all will be correct with the new def, I'll happily keep the old ID. But if we don't get a response, it'll feel safer to use a new ID.

For GO:0030363-30365, the literature I looked at didn't give me any good leads on how activity terms might be worded or defined. For 30364 and 30365 in particular, the complex terms in component (5847 and 5848, respectively) seem to capture everything that's known. If you find something I missed, though, that would make a difference.

m

Original comment by: mah11

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Hi Midori,

Thanks for the extension to look into these three:

pre-mRNA cleavage factor activity ; GO:0030363 [6] cleavage and polyadenylylation specificity factor activity ; GO:0030364 [58] cleavage stimulation factor activity ; GO:0030365 [0]

I don't see anything either that suggests a specific function, and as you say, for 30364 and 30365, the complex terms describe these complexes quite well, so I've no objection to obsoleting them either. Thanks again for the extra time.

-Karen

Original comment by: krchristie

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For the record: mailing list fodder indicated that the new wording and def would not work for all existing annotations to GO:0008248, so it has been made obsolete, with a comment mentioning the new term:

RNA splicing factor activity, transesterification mechanism ; GO:0031202

Parentage has been adjusted according to Karen's proposal.

GO:0030363, 30364, and 30365 alos made obsolete as described below.

Thanks to everyone who commented on this item or responded via the mailing list.

m

Original comment by: mah11

[gocentral]

• labels: --> Term obsoletion
• milestone: --> 224410
• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11