Jacob,
So you'd have to explain why the codon convention is so
intolerant/invariant relative to the other features--it seems to me
that either it is at an optimum or there is some big barrier holding
it in place.
Because altering codon convention will result in massive translation errors.
However the original question refers to start codon and its relation to
methionine. Notice that AUG is the *only* codon for methionine. If you
change amino acid specificity of the methionine tRNA synthetase, you'd
replace every methionine in every protein. It is very unlikely that an
organism other than one with a very small genome can survive that.
Given high fidelity required of tRNA synthetases, changing their
specificity is also not easy. Most mutations are likely to incapacitate
the enzyme rather than switch its specificity, resulting in organism
that is unable to develop (due to stalled translation), let alone survive.
As for the optimization part - I am also not sure what significant
benefit you expect from replacing starting methionine with a different
amino acid. It is mostly removed anyway. Why that is? My (uneducated)
guess is that it is rarely structural and there is benefit in recycling it.
Cheers,
Ed.
