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

[Ingrid Keseler]

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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>>
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