(none) (Horizontal gene transfer)

Simon Topp Simon_Topp-1 at sbphrd.com
Tue Jun 24 05:35:00 EST 1997


Andrew J. Roger wrote:
> 
> I totally disagree with you.  E.coli has three genes that are closely
> related to GAPDH named Gap A-C.  E. coli GAPA  falls with an enteric
> gamma-proteobacterial clade of GAP genes which are together located
> within the eukaryotic GAPDH clade.  This is not at all a straightforward
> placement for these enzymes- I believe that two explanations are still
> open. 1) the enteric GAPA clade is derived from a lateral gene transfer
> from the eukaryotic lineage OR 2) there is a eubacterial family of GAPA
> proteins which has been lost from many taxa but retained in enterics,
> cyanobacteria, and bacteroides- the eukaryotic enzyme is in this case
> suggested to be derived from a lateral transfer from the proteobacterial
> lineage (the mitochondrial endosymbiont perhaps).  On either explanation
> I doubt one could suggest that the enteric group is in a "perfect
> taxonomic position". There are deep problems with GAPDH trees (look at
> the position of the Trichomonas vaginalis GAPDH for instance)-- some of
> this
> may be due to lateral transfer and some of it probably is due to
> paralogy.
> 

In my haste to post a short message without going into detail I was
perhaps a little too flippant in some of my comments. Doolittle's paper
concentrated on the E.coli GAPA gene and placed it firmly within the
eukaryotes. I was claiming that this particular gene was in its correct
taxonomic position, along with all the other enteric bacterial GAP's.
E.coli GAPB & GAPC are placed with the non-enteric bacteria, suggesting
some form of transfer has taken place with these genes and not with
GAPA. 
 I would question  your conclusion that "E. coli GAPA  falls with an
enteric gamma-proteobacterial clade of GAP genes which are together
located within the eukaryotic GAPDH clade" as my analysis shows the
trees to divide clearly between prokaryotes and eukaryotes with no
overlap. In fact there is a clear ordered distinction between coliforms,
non-coliforms, fungi, plants, vertebrates and invertebrates.
I would be interested to know why you believe that the enteric clade is
situated within the eukaryotes, as the whole discussion seems to hang on
this point. If they do not, then there is certainly evidence for gene
transfer between bacteria, but the evidence for horizontal gene transfer
is weakened.

Best wishes
Simon



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