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progenitor gene

J. Peter Gogarten Gogarten at UConnVM.UConn.edu
Thu Jun 19 11:45:56 EST 1997

Extreme thermophiles appear to have lower substitution rates in their
rRNA genes.  In case of proteins the difference in rates is less
obvious, however, preliminary analyses that I did on ATPase genes
suggests that the among site rate variation is much higher thermophiles,
i.e. thermophiles have more sites that change only slowly or not at
all.  My (and others, although certainly not everyone agrees) guess is
that both effects have the same cause: for a protein or a nucleic acid
to be stable at high temperatures (i.e. to not unfold) it needs more 3-D
interactions in the macromolecule than at lower temperature, thus there
are more constraints on more sites (the sites that form these
cross-links).  Along these lines one could conclude that macromolecules
in extreme thermophiles are more similar to macromolecules in the last
common ancestor.  

The other questions is which molecules evolve slower than others.  For
the more recent evolution (as I work on the early evolution of life my
definition of recent goes back to about 3 billion years before the
present) vacuolar, archaeal and F-ATPase catalytic and "regulatory"
subunits are an excellent choice (50% sequence identity between
orthologues from archaea and eucarya).  The problem is that they
underwent an ancient gene duplication, and as found with other proteins,
gene duplications are followed by a period of accelerated substitutions,
which makes them less similar to the ancestral enzyme.  This is a
catch22: you need the ancient gene duplication to provide an outgroup,
but the duplication event yields higher substitution rates.  May be
proteins in which the products of the gene duplication do not interact
with each other show less of a rate acceleration. 

`	Peter Gogarten 

 ThetherFrancois JEANMOUGIN wrote:
> In article <5nmais$n7g at ruacad.runet.edu>,
>         rkliman at runet.edu (Richard M Kliman) writes:
> [...]
> > My apology to the original poster: I'm afraid I've said nothing that will
> > help you, or anyone else, identify an extant gene that is most similar to
> > the first gene found in a living organism.  I'll leave it to others to
> > argue about whether or not an extant organism is most similar to the
> > common ancestor of all extant organisms.
>         I think I understood what you mean. Perhaps then the original
> question can be : Is there species which where placed in such
> ecological niche in such selection pressure condition so that
> not much mutation can be fixed?
>         Do you have any idea of an ecological niche or organism
> that will fit this question?
>         Well, if I could ask the question, I can't answer ;-).
>                                                         Francois.
> --
> Francois Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
> tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
> e-mail : jeanmougin at igbmc.u-strasbg.fr
> "C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun."(Thiefaine)

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