You may want to read:
Evolutionary conservation of codon optimality reveals hidden signatures of
cotranslational folding
Nature structural & molecular biology VOLUME 20 NUMBER 2 FEBRUARY 2013 237
Here they suggest that the codon bias is such it allows translation to pause
and folding of the polypeptide. Most proteins probably do not have a problem
folding so it does not matter which codon is used.
Dan
It is so intolerant to change because reassigning a codon to a different amino
acid type or stop codon affects thousands of proteins that use that codon
simultaneously. The probably that none of those mutations are deleterious is
extremely small.
Genetic code changes are more common in the mitochondrial code. First of all
the mitochondrial genome is much smaller, ~16kb for vertebrates. Moreover, in
cases I have looked at the change in codon use seems to happen when first there
is a case of extreme bias against using a codon. When a codon is (almost) not
used at all it can be re-purposed without affecting any proteins.
Bart
On Tue, Mar 19, 2013 at 2:05 PM, Jacob Keller <j-kell...@fsm.northwestern.edu>
wrote:
I don't understand this argument, as it would apply equally to all features
of the theoretical LUCA
No it won't. Different features would have different tolerance levels
to modifications.
Yes, this "tolerance" is the second (hidden or implicit) principle I
referred to. 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. And you'd
have to explain this without invoking interchange of DNA, viruses, etc, as
we're talking about a LUCA here, right? And you'll have to make sure that
whatever reason you invoke cannot be applied to other features of this LUCA
which are indeed seen to be variable.
JPK
