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HSP70 phylogeny

S. LaBonne labonnes at csc.albany.edu
Thu Dec 22 11:55:33 EST 1994

In article <3dc4pe$lg1 at mcmail.cis.McMaster.CA>,
G. Brian Golding <golding at mcmail.cis.mcmaster.ca> wrote:

>Dr. LaBonne has written ...
>    And why should we choose to believe _that_, when there are many
>    sequences that _do_ support the Iwabe et al. rooting?
>    [demonstrating a relationship between the eukaryotes and the
>    archaebacteria]  Allow me to refer you also to the Doolittle and
>    Brown symposium paper (PNAS 91:  6721-28, 1994).
>(the phrase in square brackets is our addition).
>Well ..., we don't want to contradict clear data that have been well
>established.  So any hypothesis that explains the HSP70 data must not
>contradict this data.  How is this possible?  
>As we tried to explain in our paper (obviously unsuccessfully), there
>is a hypothesis which permits both.  This hypothesis, which was
>originally proposed by Professor W.Zillig (Current. Opin. Gent. Devel.
>1:544-551, 1991) suggested that the eukaryotic cell nucleus is derived
>by superimposition or a combination of an archaebacterial and a
>eubacterial genome.  By selection of some genes from the archaebacteria
>to continue in the eukaryotic lineage - you would arrive at one tree;
>by selection of some genes from the eubacteria to continue in the
>eukaryotic lineage - you would arrive at another tree.  The HSP70 data
>suggests that the eubacteria was a gram negative bacteria and Dr. Jim
>Lake's results suggests the archaebacteria was perhaps an eoocyte.

Well, a less strong, and less glamorous way to put this is simply to
note that horizontal gene transfer is frequent in prokaryotes, and
that one would thus expect to see a number of gene trees which are
apparently inconsistent with the true organismal tree.  It seems to
me premature to claim that the mixing is _so_ thorough that talk
of a chimera is appropriate.  Perhaps soon there will be sufficient
data to evaluate this hypothesis more thoroughly, but the time is
not yet.

>Dr. LaBonne continues ...
>    None of the possible universal trees can be refuted by a single
>    gene phylogeny; if such a procedure were accepted we would have to
>    conclude that they have _all_ been falsified.  What then- special
>We do not advocate special creation.  Dr. Gogarten kindly provided a
>list of other genes which also show this relationship.  His list from a
>previous post can be summarized with shortened references as ...

[list deleted] Yes, just as I said: there have been claims of sequence
sets that support _each_ of the possible relationships; I have already
given a reference that contains such a list.  Perhaps I am just
suffering from a molecular biologist's bias, but I am strongly
impessed by the now well-established fact that the eukaryotic
transription machinery has essentially been carried over bodily from
the archaea.  Together with the fact that DNA polymerase is one of the
genes that firmly support the archaea-eukarya relationship, this means
that the basic genetic apparatus of eukaryotic muclei is entirely of
archaeal origin.  With a fairly short list of genes supporting the
gram negative- eukaryotic relationship, it seems to me (a plain old
molecular biologist and outsider to this field, who thus has no ax to
grind) that talk of chimeras is rather premature in the current state
of the data.  What I see at this time is strong support, not yet
amounting to proof, that the eukaryotic nuclear lineage is essentially
of archaeal origins, with a significant minority of genes that seem
to have been acquired from the bacterial lineage via horizontal
transfer.  Of course, the difference between this and the interpretation
you present is essentially one of nuance.

Steve LaBonne *********************** (labonnes at csc.albany.edu)
"It can never be satisfied, the mind, never." - Wallace Stevens

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