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Is Carl Woese losing a Kingdom?

Arlin Stoltzfus arlin at is.dal.ca
Fri Oct 4 08:05:30 EST 1996

L.A. Moran wrote:
> Peter Gogarten writes,
> >It seems to me that Gupta (and others) are throwing out the child with
> >the bath-water. The finding that all archaebacteria studied so far contain
> >many genes that are similar to their eukaryotic counterparts and that these
> >archaebacterial genes are very dissimilar to their homologues found in
> >other prokaryotes certainly sets the archaebacteria as a group clearly and
> >distinctly apart from all of the eubacteria.
> Turns out that there actually aren't many genes that fall into this catagory;

Perhaps you could tell us what are the proportions.

> >That some genes (e.g. HSP70s and glutamine synthetases) do not reflect a
> >"fundamental distinction" between archae- and eubacteria cannot and should
> >not be ignored; however, one can hardly take these genes and ignore all the
> >characters that define the archaebacteria as a distinct group and claim the
> >archaebacteria should be considered a part of the gram positives.
> Nor should one take the other genes on faith and claim that the
> archaebacteria should be considered a part of the eukaryotes. Keeping an
> open mind means avoiding unnecessary rhetoric in favor of any hypothesis,
> for now.

Its not quite as simple as that.  In my opinion, one is perfectly 
justified in being skeptical of phylogenetic trees.  Until we know
how reliable they are, we shouldn't trust any one of them too much.
However, to the extent that we mistrust protein trees as indicators of 
true organismal geneology, we should also mistruct contradictions 
between the trees.  That is, if you really doubt the validity of
protein trees, then it is rather premature for you to insist so
vociferously that the "conventional" view has been disproven.  How
can anything be disproven by these unreliable trees?  What if the
contradictions are only noise?  What if they are due to paralogy?  

> [BTW, those characters that define the archaebacteria as a distinct group
> could mean that they are a distinct group *within* the prokaryotes. No
> one is claiming that the archaebacteria are gram positive bacteria.]

What do you mean by "prokaryotes"?  It is obvious to anyone who
knows the definition of 'prokaryote' that archaebacteria are prokaryotes
(even Woese stopped claiming that archaebacteria weren't prokaryotes
10 years ago).  Presumably you mean "eubacteria" when you say this, but
the notion that archaebacteria are distinct from eubacteria is not merely 
supported by questionable phylogenetic trees. It is also the case that they
have RNA polymerase enzymes and (apparently) transcription initiation similar
to that of eukaryotes.  That is, they have eukaryotic-like TFs, and
not the sigma factors found in cyanobacteria, proteobacteria and gram+
bacteria.  This doesn't tell us whether archaebacteria are a sister
group to eukaryotes, but it does contradict the idea that they are 
a subgroup of eubacteria. 
> >Category 1: genes that were contributed to the eukaryotic cell either via
> >the mitochondrial endosymbiont (R. Hensel and F. Doolittle think that many
> >glycolytic enzymes belong into this category)
> No question that some genes have been transferred to the nucleus from
> mitochondria and chloroplasts. To suppose that many glycolytic enzymes
> belong to this catagory is, in my opinion, based on wishful thinking.

Fortunately, we won't have to rely on your opinion for long.  There will 
be some work published on this subject later this year from Bill Martin's 
group and from Patrick Keeling of the Doolittle lab.  We can try to draw them
into this discussion if you want to find out more.

> The "eukaryocentric" perspective is that which assumes that eukaryotes are
> somehow later arrivals on the evolutionary scene and that the origin of
> the eukaryotic cell has to be explained by a fusion of two types of
> prokaryotic ancestor.

This is wrong on two counts.  First, it is not some quirky societal bias
to suppose that prokaryotic cells preceded eukaryotic ones.  One may
question whether the assumption is truly ironclad, but it amounts to 
nothing more than to suppose that cells having their genes enclosed 
within a nucleus arose from cells with their genes not enclosed
within a nucleus.  There is nothing 'eukaryocentric' about this, it is
simply a suggestion that this particular type of transition can be polarized
(i.e., we can infer the primitive condition without knowing the phylogeny). 
 This doesn't mean that we will necessarily find the prokaryotic group 
that gave rise to the eukaryotes, or that the pre-eukaryotes must 
correspond to some recognizable group of modern prokaryotes.  

Second, it is hardly a common assumption that the origin of the eukaryotic
cell has to be explained by a fusion of two types of prokaryotic ancestor.
This predilection has only arisen in the last 5 years or so, specifically
in the literature of archaebacteriologists and molecular types.  Before
that, not even Margulis (who exaggerates the importance of symbiosis
_ad nauseam_) believed that the nucleus was an endosymbiont!  It simply
doesn't help to explain the peculiar properties of the nucleus (its
continuity with the ER, its double membrane structure, its pores, 
its relationship to ribosome assembly, its mode of division, etc, etc)
to propose that it is the remnant of an endosymbiont. 

> There may not have been major horizontal transfer (fusion) events
> associated with the emergence of eukaryotes. We'll have to wait and see.


Arlin Stoltzfus
Department of Biochemistry
Dalhousie University
Halifax, Nova Scotia B3H 4H7 CANADA
(email) arlin at is.dal.ca 
(phone) 902-494-3569 
(fax) 902-494-1355

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