Just search for genetic code evolution in pubmed and you will find tons of literature on it. The main driving force appears to have been to minimize physico-chemical changes in amino acid properties for frequent mutations. In other words, if you take mutation rates at the single-nucleotide level and use it to predict, via a codon table, the rates of amino acid mutations you will find that it correlates strongly with the observed amino acid rates.
Bart On Tue, Mar 19, 2013 at 8:34 AM, Jacob Keller < [email protected]> wrote: > Never one to shrink from philosophizing, I wonder generally why the codon > conventions are the way they are? Is it like the QWERTY keyboard--basically > an historical accident--or is there some more beautiful reason? One might > argue that since basically all organisms share the convention (are there > exceptions, even?), that it must be the "best of all possible" conventions. > I have often wondered whether maybe this particular convention allows for > the most effective pathways between proteins of significant function, e.g., > through the fewest mutations perhaps? One certainly cannot maintain that > every possible protein sequence has been made at some time or another in > the history of the biological world (go quantitate!) so there must be a way > to ensure that mostly the "best" ones got made. On the other hand, since > many organisms share DNA, maybe they had to "agree" on a system (I think > this is the dogma?). Was there a "United Organisms" convention at some > point, reminiscent of "Les Immortels" of the French language or POSIX or > something, to ensure compliance? What was the penalty for non-compliance? > > Anyway, I like the question about the methionines, > > Jacob > > On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry <[email protected]>wrote: > >> Opher Gileadi wrote: >> >>> Hi Theresa, >>> >>> To add to Anat's comments: Although the AUG codon for the first >>> methionine and all other methionines in a protein coding sequence look the >>> same, they are read in a very different way by the ribosomal machinery. The >>> first AUG is recognized by the initiation complex, which includes the >>> separate small ribosomal subunit (40s), a special tRNA-methionine, and >>> initiation factors (proteins) including eIF2. This leads to assembly of a >>> complete ribosome and initiation of protein synthesis. Subsequently, in the >>> process of elongation, AUG codons are read by a different tRNA, which is >>> brought to the 80s ribosome bound to a protein called elongation factor 1a. >>> This is an oversimplification, of course, but the point is that the >>> initiation codon (=the first amino acid to be incorporated to the protein) >>> is read by a special tRNA, hence the universal use of methionine. >>> >>> Opher >>> >>> Yes, but why methionine? Half the time it has to be removed by >> N-terminal peptidase to give a small first residue, or by leader sequence >> processing. Why use a big expensive amino acid instead of choosing one of >> the glycine codons? Is there an obvious reason, or just "it had to be >> something, and Met happened to get selected"? >> >> And why sometimes alternate start codons can be used? and why doesn't >> initiation occur also at methionines in the middle of proteins? I'm >> guessing it has to do with 5' untranslated region and ribosome binding >> sites. So could the start codon actually be anything you want, provided >> there is a strong ribosome binding site there? >> >> Just being philosophical, and not afraid to display my ignorance, >> eab >> > > > > -- > ******************************************* > > Jacob Pearson Keller, PhD > > Looger Lab/HHMI Janelia Farms Research Campus > > 19700 Helix Dr, Ashburn, VA 20147 > > email: [email protected] > > ******************************************* > -- Bart Hazes Associate Professor Dept. of Medical Microbiology & Immunology University of Alberta
