[Fwd: Re: [annotation] RNA trimethylguanosine cap binding query]
Alexander Diehl
adiehl at informatics.jax.org
Thu Jan 17 02:56:16 PST 2008
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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> 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.
>>>
>>>
>>
>>
>>
>>
>
>
>
--
Alexander Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
email: adiehl at informatics.jax.org
work: +1 (207) 288-6427
fax: +1 (207) 288-6131
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