[BiO BB] overlapping/shadow genes in prokaryotes

[Timothy Driscoll]

On Dec 14, 2005, at 3:23 p, Martin Gollery wrote:

> hi Tim,
>
> Are these predicted genes in the same reading frame, or is there a  
> frameshift between them?
>
> Best regards,
> Marty
>
hi Marty,

thanks for the response.  actually, I should have been more specific  
- the predicted genes run on opposite strands.

so far, I have curated approximately 125 genes (not counting the  
overlappers) of one megaplasmid of this genome (admittedly, a very  
small fraction of the total genome).

23% of the curated genes are paired with predicted overlapping genes.
all of the pairs are on opposing strands.
all overlaps are substantial - generally the entire gene, or most of it.
38% of the pairs are in the +1/-2 orientation.
28% of the pairs are in +1/-1 orientation.


AFAIK, overlapping genes in this fashion is a common mechanism for  
genome compaction in prokaryotes.  so there would be no reason to  
rule out one of the two overlapping genes, simply because it overlaps  
another gene - unless, of course, the supporting evidence is  
particularly poor.  IOW, both predictions could very well be correct,  
and the fact that they overlap has no bearing on whether they are  
'real' genes.  is that a fair statement?

thanks,

tim


> On 12/14/05, Timothy Driscoll <molvisions at mac.com> wrote:
> hi,
>
> how prevalent is gene overlap in prokaryote genomes?  not just a few
> codons at one end, but large regions of overlap, sometimes as long as
> the complete gene.  I have recently begun curating the genome of a
> Gram-negative bacteria. I am finding a lot of predicted overlapping
> genes (Genemark, Glimmer, RefSeq), often with roughly equivalent
> supporting evidence in favor of both genes (Blast hits, RBS, codon
> bias, etc.).
>
> I have been told that overlapping genes are uncommon, and never more
> than about 30 codons in the overlap. but I am unable to find any data
> to support this. can anyone please provide some helpful references?
>
> many thanks,
>
> tim
> --
> Timothy Driscoll                                em: molvisions at mac.com
> molvisions - see. grasp. learn.                 ph: 919-368-2667
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>
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> -- 
> Martin Gollery
> Associate Director
> Center For Bioinformatics
> University of Nevada at Reno
> Dept. of Biochemistry / MS330
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-- 
Timothy Driscoll                                em: molvisions at mac.com
molvisions - see. grasp. learn.                 ph: 919-368-2667
<http://www.molvisions.com/>                    im: molvisions
usa:virginia:blacksburg                         tx: molvisions at vtext.com