A cause for reduced translation efficiency in E.coli?

[Trond Erik Vee Aune]

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