[go] ISA/ISO

[Pankaj Jaiswal]

This seems like a case for 'functional ortholog' based on the conserved 
assembly and interaction among subunits of a protein complex from two 
different species. We see these cases quite often.

Here is an interesting paper on this theme
Systematic identification of functional orthologs based on protein 
network comparison. Genome Res. 2006 Mar;16(3):428-35.
PMID: 16510899
http://www.ncbi.nlm.nih.gov/pubmed/16510899?dopt=Abstract

Pankaj


Gwinn Giglio, Michelle wrote:
> 
> 
> 
> Hi Val,
> 
> The definition of ortholog is that the two sequences arose from a common
> ancestor and were separated by a speciation event.  The situation you
> describe sounds to me like there is good evidence that the two proteins
> carry out the same functions, however they could either be orthologs that
> have diverged so much that no recognizable sequence similarity remains or
> they have arisen due to convergent evolution and are NOT true orthologs.
> 
> Michelle
> 
> 
> 
> 
> On 2/21/08 8:54 AM, "Valerie Wood" <val at sanger.ac.uk> wrote:
> 
>> In support of the final sibling arrangement of ISA/ISO, I came across an
>> example today where gene products are known to be orthologous but have
>> no sequence conservation which I thought I would share.
>>
>> Identification of the Proteins, Including MAGEG1, That Make Up the
>>  Human SMC5-6 Protein Complex
>> Elaine M. Taylor, Alice C. Copsey, Jessica J. R. Hudson, Susanne Vidot,
>> and Alan R. Lehmann
>> quote
>> "Nse6 contains ARM/HEAT repeats, but there is no sequence conservation
>> between these presumed orthologs from S. cerevisiae/ and /S. pombe/. In
>> /S. pombe/ they also appear to bridge the head domains of Smc5 and Smc6"
>>
>> where it is not even possible to detect the similarity between the 2
>> nse6 subunits in yeast and pombe but they are presumed orthologs from
>> other biological properties and position in the complex, binding
>> partners etc.
>> These are NOT reciprocal best hits, and although they can be aligned,
>> (you can align anything) it does not mean, that if I inferred any
>> experimental data from the S. cerevisiae ortholog it would come from a
>> sequence alignment.
>>
>> I should also add that this is very common which also has large
>> implications for the orthology prediction exercise.
>>
>>
>> Val
>>
>>
> 
> 

-- 
Pankaj Jaiswal
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Dept. of Plant Breeding and Genetics
Cornell University
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