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Evolutionary tree of *all* proteins

Laurent Duret duret at evoserv.univ-lyon1.fr
Wed Oct 12 02:38:41 EST 1994

> In article <DRW.94Oct6155502 at taylor.mit.edu>, drw at taylor.mit.edu (Dale R. Worley) writes:
> |> One can now make family trees of sequenced proteins.  In some cases,
> |> the roots of these trees extend back far enough to be interesting, in
> |> some cases, the divergence of the eukaryotes or before.  Since, in
> |> theory, all modern proteins are descendents of a handful of primal
> |> proteins, once you take the ancestries of proteins back far enough,
> |> you should start to see family resemblances between proteins that
> |> don't have much resemblance now, and the beginnings of the Big
> |> Picture:  the family tree of ALL proteins.
> |> 
> |> Do we have enough data to do something like this yet, and if so, what
> |> does the family tree look like?

In addition to the relevant comments made by Georg Fuellen 
(fuellen at dali.Mathematik.Uni-Bielefeld.DE) we have to mention that the establishment
of such tree is further complicated by the fact that many proteins are composed of
"domains" (or "modules") that have different evolutionary origins and histories.

For example, a protein gene may have evolved by fusion of two genes, exchange of exon,
etc.  This mode of evolution is frequently observed, particularly among higher eukaryotes (probably because of the interuption of genes by introns). For a recent 
review, see Patthy 1994, Curr. Opin. Struct. Biol. 4:383-392.

Suppose that protein AB arose by fusion of protein A and protein B, that protein
AC arose by fusion of protein A and protein C and that protein BC arose by fusion of 
protein B and protein C.

AB, AC and BC share homology. However, these homology relationships can not be
represented by a tree.

Therefore, it is not possible to construct "family tree of ALL proteins". Maybe,
we could try to construct a tree of all protein DOMAINS.

Best regards,


Laurent Duret			    duret at biomserv.univ-lyon1.fr
Tel: 	+33		    Fax:	+33
Laboratoire de Biometrie, Genetique et Biologie des Populations
Bat 741 - URA CNRS 243 Universite Claude Bernard - Lyon I
43, Bd du 11 Novembre 1918 
69622 Villeurbanne cedex FRANCE

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