A cause for reduced translation efficiency in E.coli?

[Zhonglin Chai]

MFOLD developed by Dr. Zuker would do the job for you. The website is 
http://bioweb.pasteur.fr/seqanal/interfaces/mfold.html

You will find out that most of mRNA molecules are almost entirely
hybridized with themselves although some small loops are always
present.



Zhonglin Chai, PhD

Molecular Hypertension Laboratory
Baker Heart Research Institute
Commercial Rd, MELBOURNE, VIC 3004
AUSTRALIA

Post Address:
P.O. Box 6492
St.Kilda Road 
Central Melbourne 
VIC 8008, AUSTRALIA

Telephone: +61 3, 8532 1231
mobile : 0413 58 1940, or international +61, 413 58 1940
Fax: +61 3, 8532 1100 
email: zhonglin.chai at baker.edu.au


>>> Trond Erik Vee Aune
<trondaun at chembio.REMOVETHISBEFOREREPLYING.ntnu.no> 08/26/02 06:57pm
>>>
Hi,

Is there a possibility that lowered translation efficiency can be
caused 
by hybridization of the RNA to itself? If, for instance, a part of the

gene hybridizes with a part of the 5' UTR (untranslated region) in such

a way that ribosome binding is hindered? (I assume that hybridizations

that does not partly overlap the ribosome binding site would not affect

translation since the ribosome would be able to break up the binding)

It could be that a single RNA molecule folds over and hybridizes with 
itself, or, in cases with good transcription, that two different (but 
still from the same transcript) RNA molecules binds to each other.

I know the fact that transcription and translation in E.coli is coupled

  diminishes this possibility, but I think that the ribosome binding 
site with its surrounding regions partly would be free for such 
interactions, especially with other RNA molecules.

I also know that this would probably not be a problem with native
E.coli 
transcripts, but in cases with homologues expression, where the gene
and 
the untranslated region come from different sources, I think this may 
contribute to lowered translation when all other possibilities are 
exhausted.

Do you know of any programs that can analyze RNA sequences looking for

hybridization possibilities?

Regards,
Trond Erik Vee Aune

http://www.chembio.ntnu.no/molgen 



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