[Annotation] [Gohelp] GO term for "anti-adaptor" protein

[Valerie Wood]

Hi Ingrid

In that case, it looks as though the term you require is
anti-sigma factor antagonist activity ?
http://www.ebi.ac.uk/ego/GTerm?id=GO:0043856

However, if this does not bind to the transcription factor or the 
promoter it seems that the parentage 'transcription regulator activity' 
is incorrect? It may need to move under binding.

anybody else got any input here?

Val


Ingrid Keseler wrote:
> Hi Val,
>
> Thanks for the input - I had been applying the "no function term 
> unless you know the mechanism" rule subconsciously, in a way.  In this 
> case, though, the mechanism seems fairly clear.  What you annotated 
> recently sounds just like the RssB protein in E. coli; what I'm trying 
> to annotate are regulators of RssB (the "sigma factor antagonist" of 
> sigmaS).  So the ultimate effect of the Ira proteins is that of 
> transcription activators (negatively regulating a negative regulator), 
> but I have never thought of proteins that act indirectly as 
> transcription factors.  To me, a transcription activator/repressor is 
> a protein that binds DNA or the polymerase; I wouldn't have even 
> thought to annotate RssB itself to that term.  Although in analogy 
> with metabolic pathways, say tryptophan biosynthesis, the first enzyme 
> in the pathway does not synthesize tryptophan itself.  So are you 
> saying that this can be thought of as a regulatory pathway, ultimately 
> leading to higher levels of transcription by sigmaS polymerase?  I 
> would still think of this more in terms of process than function.
>
> -Ingrid
>
> Valerie Wood wrote:
>> Hi Ingrid,
>>
>> I don't know much about E. coli but I annotated something similar for 
>> pombe last week (a gene which negatively regulates a transcription 
>> factor by promoting its degradation).
>> I did not annotate a molecular function for this, but the mechanism 
>> is unknown (even interaction has not yet been demonstrated). The 
>> general rule I use  is, that if you do not know the mechanism, then 
>> you do not use a function term (i.e transcriptiional regulator, or 
>> enzyme regulator or one of its children), but make only a process 
>> term.  Here you seem to have more information
>>
>> transcription repressor activity
>> http://www.ebi.ac.uk/ego/GTerm?id=GO:0016564
>> Any transcription regulator activity that prevents or downregulates 
>> transcription.
>>
>> Val
>>
>>
>>
>>
>> Eurie Hong wrote:
>>> Hi Ingrid,
>>>
>>> I'm cc'ing your question to the annotation mailing list.  There are  
>>> many GO curators who annotate a wide range of species on this 
>>> mailing  list so this is probably the best list for you to email 
>>> regarding  annotation questions.
>>>
>>> Here is information to subscribe to the mailing list if you are not  
>>> already on it:
>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>
>>> Cheers,
>>> Eurie
>>>
>>> On Apr 30, 2008, at 2:27 PM, Ingrid Keseler wrote:
>>>
>>>  
>>>> Hi everyone,
>>>>
>>>> I'm having a difficult time identifying an appropriate GO function  
>>>> term
>>>> to annotate a set of small so-called "anti-adaptor" proteins in E.
>>>> coli.  Here's what they do: under normal conditions, a protein called
>>>> RssB binds to the alternative sigma factor, sigmaS, and targets it for
>>>> degradation by the ClpXP protease.  Under certain environmental
>>>> conditions, e.g. phosphate starvation, DNA damage etc., certain small
>>>> proteins (IraP, IraD, IraM) are expressed; they bind to RssB, thus
>>>> (maybe just by competition) preventing it from binding to sigmaS, and
>>>> therefore sigmaS accumulates.  For illustration, see Fig. 6 in PMID
>>>> 18383615 or Fig. 6 in PMID 16600914 (free access).  What would you  
>>>> call
>>>> that function?  I already have GO:0005515 protein binding for the
>>>> interaction with RssB, but that doesn't convey the actual 
>>>> function.   For
>>>> process, I am using GO:0042177, negative regulation of protein  
>>>> catabolic
>>>> process.
>>>>
>>>> Any ideas?  Thanks!
>>>>
>>>> -Ingrid
>>>> _______________________________________________
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>>>> Gohelp at geneontology.org
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>>>>     
>>>
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>>>
>>>
>>>   
>>
>>
>
>
>


-- 
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Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
Wellcome Trust Genome Campus	 http://www.genedb.org/genedb/pombe 
Hinxton, Cambridge, CB10 1HH	 http://www.sanger.ac.uk/Projects/S_pombe



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