[Fwd: Re: [annotation] RNA trimethylguanosine cap binding query]
Alexander Diehl
adiehl at informatics.jax.org
Thu Jan 17 06:41:44 PST 2008
Harold,
A quick google of "convalent binding" yields lots of hits, mostly of a
scientific nature. I think this is a not-uncommon usage, undergraduate
chemistry be damned.
-- Alex
Harold Drabkin wrote:
> 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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>>> 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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