'protein processing' - update definition

[gocentral]

Hi,

I started this discussion on the annotation email list and posting the message here for further action.

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Hi all,

I'm annotating a gene that encodes a methionine aminopeptidase, one of the enzymes involved in removing the N-terminal methionine of many proteins.

I found the function term without any problem but am having some questions about what process term to use. From looking at other genes annotated to 'methionyl aminopeptidase activity GO: 0004239', they are annotated to the process term 'proteolysis and peptidolysis.'

proteolysis and peptidolysis: Destruction of a protein or peptide by hydrolysis of peptide bonds.

I'm tempted to use the term 'protein processing' instead because of its less 'destructive' definition.

protein processing: The post translational modification of a protein, particularly secretory proteins and proteins targeted for membranes or specific cellular locations.

However, from the paper I'm reading (PMID:11060042), the process itself is not POST-translational but rather CO-translational.

"Two enzyme families are involved in the co-translational process of methionine removal, methionine aminopeptidase (MAP) and peptide deformylase (PDF) (for reviews see Meinnel et al., 1993b; Bradshaw et al., 1998; Giglione et al., 2000)."

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? cmd=Retrieve&db=PubMed&list_uids=11060042&do pt=Abstract

Should the definition of 'protein processing' be amended and new child terms 'co-translational protein processing' and 'post- translational protein processing' be created?

Thanks,

Tanya

Reported by: tberardini

Original Ticket: "geneontology/ontology-requests/1900":https://sourceforge.net/p/geneontology/ontology-requests/1900

[gocentral]

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Harold's reply:

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Hi Tanya NME (N-terminal methionine excision) is co-translational in vivo. I've just checked with my "expert" in the field from MIT, and he concurs. Thus, I think we do need to fix the def and perhaps split into co and post- Translational processing.

Original comment by: tberardini

[gocentral]

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Hi,

How would this do:

protein processing ; GO:0016485 def: The post translational modification of a protein, particularly secretory proteins and proteins targeted for membranes or specific cellular locations.

change to:

post-translational protein processing ; GO:0016485 def: The post-translational modification of a protein, particularly secretory proteins and proteins targeted for membranes or specific cellular locations.

new terms:

protein processing ; GO:new def: The modification of a protein, particularly secretory proteins and proteins targeted for membranes or specific cellular locations.

co-translational protein processing ; GO:new def: The co-translational modification of a protein, particularly secretory proteins and proteins targeted for membranes or specific cellular locations.

protein modification ; GO:0006464 -%protein processing ; GO:new --%post-translational protein processing ; GO:0016485 --%co-translational protein processing ; GO:new

Jen

Original comment by: jenclark

[gocentral]

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Do we need to keep the bit about '...particularly secretory proteins and blah, blah, blah'? For the removal of the N-ter methionine, I don't think that this is particularly for secreted or targeted proteins but for almost all proteins in the cell.

Tanya

Original comment by: tberardini

[gocentral]

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Hi,

Is this better? (With the contents of the brackets appropriate to each term.)

The [...]translational modification of a protein.

Jen

Original comment by: jenclark

[gocentral]

• assigned_to: nobody --> jenclark

Original comment by: jenclark

[gocentral]

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John Garavelli says can we hang on until he comments in a week's time after he's been away to a conference.

Jen

Original comment by: jenclark

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I agree that we should remove the blahdiblah about secreted proteins. We're trying to explain what the process is, not necessarily what the substrates are. With that in mind, we really need to improve the existing and proposed new definitions: the ones in this entry (including the one that's been in all along) just restate the term name, and do no defining at all.

m

Original comment by: mah11

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• assigned_to: jenclark --> nobody

Original comment by: jenclark

[gocentral]

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any progress on this?

I think what we need to do is figure out what the distinction is between 'protein processing' (16485) and 'protein modification' (6464). The existing definitions are not exactly enlightening, although the definition of protein modification is much better than that of protein processing:

'The covalent alteration of one or more amino acid residues within a protein, resulting in a change in the properties of that protein.'

m

Original comment by: mah11

[gocentral]

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See also SF:1150967 'Notch receptor processing ; GO:0007220', where we need to know what the difference between protein modification and protein processing is, to know if/how far the definition of GO:0007220 should be broadened.

Original comment by: beckyfoulger

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item [ 1232819 ] protein processing closed and moved here:

https://sourceforge.net/tracker/index.php?func=detail&aid=1232819&group\_id=36855&atid=440764

Original comment by: jl242

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> hjdrabkin

Original comment by: mah11

[gocentral]

This is amazingly out of date, and the definitions of protein modification, maturation, processing, etc. have all been improved (most recently just this week). Closing.

Original comment by: mah11

[gocentral]

• status: open --> closed-out-of-date

Original comment by: mah11