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Mitochondrial genetic codes

S. LaBonne labonnes at csc.albany.edu
Fri Sep 1 11:58:04 EST 1995

In article <1995Sep1.104324.40903 at ac.dal.ca>,  <aroger at ac.dal.ca> wrote:

>There is no selectively deleterious intermediate in this scenario.
>Note that evidence for such a codon reassignment would be
>extreme codon bias against using codon A.  Such a bias is
>noticed in some of the examples of codon reassignment that have bee
>found so far.

And to this excellent explanation may I just add explicitly what is
already implicit: that mitos are one of the very places where one
typically finds very minimal tRNA sets, hence extreme codon bias.  (If
memory serves, mammals have the remarkably low total of only 22
tRNA's, accomplished by extending the flexibility of codon-anticodon
pairing further than allowed by the "canonical" wobble rules.) Another
semi-relevant aside is that UGA seems to be a remarkably versatile
codon; isn't it used to code for selenocysteine in some bacteria?

Also, let's not forget that codon reassignment has been demonstrated
in the laboratory many times- every time a nonsense suppressor is
isolated! And indeed, the ease of isolating suppressors in the three
stop codons, at least in E coli, fits very well with the scenario
outlined by aroger.  Ochre suppressors, all of which as far as I know
recognize both UAA and UAG, are difficult to isolate and grow poorly,
and even at that are generally inefficient (<10%).  Amber suppressors
are easier to isolate, grow better, and are more efficient (as high as
50% in certain cases, I believe); correspondingly, UAG is the least
frequently used stop codon in E. coli.  By the way I believe I read
somewhere that UGA in _wild-type_ E. coli is actually misread by
Trp-tRNA at a non-trivial frequency.

Once again we see, in Hubert's apparent incomprehension of these
ideas, the dangers of a focus on "coding theory" unaccompanied by an
up-to-date understanding of the biology and biochemistry of the code.
Hubert's theory, to judge by the quote reproduced by aroger, predicts
that codons can't be reassigned under any circumstances, and therefore
it predicts the non-existence of suppressors!

By the way, I've taken the liberty of changing the subject heading,
since I modestly disclaim having accomplished anything that makes me
deserve to be so famous. ;-)
Opinions are mine alone; I never met a university with opinions!
Steve LaBonne ********************* (labonnes at cnsunix.albany.edu)
"It can never be satisfied, the mind, never."   - Wallace Stevens

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