[Fwd: Re: [annotation] RNA trimethylguanosine cap binding query]
Harold Drabkin
hjd at informatics.jax.org
Thu Jan 17 06:34:38 PST 2008
I don't believe there is such thing as "covalent binding". There is
covalent bonding. Perhaps it is the term GPI anchor binding" that needs
to be obsoleted and a new term, not a child of binding, be made to
properly describe whatever is going on.
hd
Alexander Diehl wrote:
> Harold,
>
> It is true I have made a number of annotations to the term 'GPI anchor
> binding' for CD24a and Thy1. I was always a bit uncomfortable about
> these annotations as they violated the idea of binding terms being for
> non-covalent bonds only, but in fact I was only following the
> precedent set by others in the GO for GPI-anchored proteins. You see
> for as long as I have been in the GO, and perhaps for much longer, we
> have had the SwissProt Keyword mapping,
>
> SP_KW:KW-0336 GPI-anchor > GO:GPI anchor binding ; GO:0048503
>
> which basically means any protein identified by SwissProt curators as
> having a GPI-anchor has been mapped to 'GPI-anchor binding'. Apart
> from CD24a and Thy1, all the other genes in MGI annotated to 'GPI
> anchor binding' are based on this keyword mapping. Looking at Amigo,
> I believe that every single experimentally based annotation to 'GPI
> anchor binding' is for a GPI anchored protein, so clearly other
> annotators use this term in this way. I would bet this term was put
> in the GO by someone who intended it to be used this way. And, as
> Karen so conveniently pointed out, the definitions of GO binding
> terms, including GPI anchor binding, do not specifically exclude
> covalent binding, so logically the annotations stand. I would also
> point out that neither the 'Annotation Guide' nor 'Molecular Function
> Ontology Guidelines' sections of the documentation on the Gene
> Ontology Consortium's official web pages exclude annotation of
> covalent binding or even mention it. We don't even exclude annotation
> of covalent binding in the much stricter MGI GO annotation guidelines
> (the written ones).
>
> However, since I know that you are now at least driven halfway up the
> wall by my argumentation, I am may be willing to compromise and
> propose that in addition to eliminating the SwissProt keyword mapping,
> that we obsolete the term 'GPI-anchor binding ; GO:0048503' itself. I
> know of no protein that binds GPI anchors specifically in a
> non-covalent way, although I agree it is a theoretical possibility,
> and the term clearly has only been a source of confusion to GO
> annotators, although the annotations are actually _useful_ for GO
> users, who might want to be able to easily find GPI-anchored proteins
> all at once. But forget about the users -- with luck they may figure
> out that 'anchored to external side of plasma membrane ; GO:0031362'
> can be used to find some GPI anchored proteins, although there is no
> SwissProt mapping to this term and this term is less specific than
> 'GPI anchor binding'.
>
> Rest assured Harold, I do not routinely annotate covalent binding,
> except in the case of 'GPI anchor binding' where I felt I was
> following the precedent of others in the GO and providing quite useful
> information to our users. Although I am open to doing so, I do not
> plan remove my experimentally correct annotations until further
> discussions of this issue have taken place.
>
> Thanks,
>
> Alex
>
>
> Harold Drabkin wrote:
>> Alex can you please look at the GPI anchor binding annotations that
>> you made here. The term should only be used for non-covalent binding,
>> not covalent attachment. Since you recently looked at the papers, you
>> are more familiar with what they were trying to show.
>>
>> hjd
>>
>>
>>
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>> Date: Wed, 16 Jan 2008 18:11:41 +0000
>> From: Valerie Wood <val at sanger.ac.uk>
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>> To: hjd at informatics.jax.org
>> CC: Valerie Wood <val at sanger.ac.uk>
>> Subject: Re: [annotation] RNA trimethylguanosine cap binding query
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>>
>>
>> *Hi Harold,
>>
>> mouse
>> Cd24a
>> uses *PMID: 14707049 for what seems to be a covalent GPI-binding
>> doesn't it?
>>
>> i'm sure there is 'mixed usage'
>>
>> or is there some other data in there (I just did a search on GPI)
>>
>> Val
>>
>>
>>
>>
>>
>> Harold Drabkin wrote:
>>
>>> Valerie Wood wrote:
>>>
>>>> I recently used the term RNA trimethylguanosine cap binding to
>>>> annotate pombe telomerase RNA and represent the fact that this is
>>>> trimethylguanosine capped, but on re-reading the definition I'm
>>>> not sure if this is correct?
>>>> Can I use this for the modification itself? or is it for gene
>>>> products which interact with a capped product?
>>>
>>> It represents some gene product that binds to the triMeG cap present
>>> on an mRNA. Not the gene product that makes the cap. A binding term
>>> should never be used for a covalent bond. Binding implies a
>>> reversible reaction at STP, with a Ka and Kd.
>>>
>>> GPI anchor binding it meant to be used for something that binds the
>>> the GPI anchor and not covalently linked to it.
>>>
>>>>
>>>> There do not appear to be any other annotations to this term
>>>> despite the fact that many RNAs are capped which is another reason
>>>> which made me suspect my usage may be wrong.
>>>>
>>>> Should the binding terms should only be used for non-covalent
>>>> modifications (although this is only in some of the binding defs?),
>>>> and does not represent the use of some terms. For instance GPI
>>>> anchor binding is used for a number of proteins which are GPI
>>>> anchored, in addition to proteins which bins the GPI moiety during
>>>> GPI anchor biosynthesis.
>>>>
>>>> Cheers
>>>>
>>>> Val
>>>>
>>>> Def:
>>>> Interacting selectively with the trimethylguanosine
>>>> (m(3)(2,2,7)-GTP) moiety located at the 5' end of some RNA
>>>> molecules. Such trimethylated cap structures, generally produced by
>>>> posttranscriptional modification of a 7-methylguanosine cap, are
>>>> often found on snRNAs and snoRNAs transcribed by RNA polymerase II,
>>>> but have also be found on snRNAs transcribed by RNA polymerase III.
>>>> They have also been found on a subset of the mRNA population in
>>>> some species, e.g. C. elegans.
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
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