Rare arginine codon

Owen McCall Owen.McCall at abbott.com
Wed Sep 16 10:10:07 EST 1998

 I made such a plasmid years ago containing the dnaY (now argU) gene.  It is
the native
coli sequence with the native promoter provided as an EcoRI insert in pAYC184
(medium copy #).  I have used it with success, as have a number of  usenet
friends with
your problem.  If you send me your mailing address, I will send you some.
Many papers
have been published describing the effect of too many AGA/AGG codons. Note
that you
also have another problem arising in the case of abutting bad-Arg codons;  not
only do
you see the "hungry codon" effect in the worst way, you also have a RBS within
coding sequence.  Another easy fix may be to try a number of coli strains;
the baseline level of this tRNA appears to differ substantially from strain to

Tomer Tishgarten wrote:

> Bryan L. Ford wrote:
> > This approach seems difficult since the imbalance of tRNA will likewise
> > influence translation efficiency of the native E. coli genes. Let me ask
> > if
> > there is any reason that you cannot modify the rare codon into a
> > preferred E. coli codon, using the quite straightforward (that is
> > *easy*) methods of site-specific or site-directed mutagenesis?  For
> > example (using data for E. coli taken from the Codon Usage Database
> > found online at http://www.dna.affrc.go.jp/~nakamura/codon.html ) we see
> > that AGG is the rarest at 1.5 per thousand, and CGA is relatively rare
> > at 3.6/k. Both can be changed into frequently used codons with single
> > base changes, that is to AGC with a usage of 15.7/k and to CGC, which
> > happens to have the highest usage of all six arginyl codons at 21.5/k.
> >
> > Let me know if you need more information about about site-specific
> > mutagenesis protocols.
> >
> > -Bryan
> Bryan,
> I did not mention that this rare arginine codon is quite frequent in our
> gene (more than 20 occurances).  I'm affraid that it might not be either
> cost or time effective to mutate the codon within the gene.
> Thanks for your input.
> Sincerely,
> Tomer

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