Is Carl Woese losing a Kingdom?

L.A. Moran lamoran at gpu.utcc.utoronto.ca
Wed Oct 2 15:50:46 EST 1996

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;
particularly genes that are "very dissimilar" to their homologues in other
prokaryotes. In most cases the distinction that you are making is weakly
supported by the data. But let's accept it for the sake of argument. It
does suggest that there is something strange about archaebacteria. [Note
that the problem is with the archaebacteria, not any other group. We'll
return to this point later on.]

>One should keep an open mind as to whether 
>the currently known archaebacteria are mono- or paraphyletic, the above 
>mentioned genes strongly argue that a major component of the archaebacteria
>is not polyphyletic with respect to the eubacteria.

Keeping an open mind is what many of us are advocating. Some dendrograms
suggest that the archaebacteria are paraphyletic and cluster within the
prokaryotes. Other dendrograms suggest that the archaebacteria cluster
with eukaryotes. We simply don't know at this point how to reconcile
the data.

>Given that deeper branching archaebacteria are being discovered, it seems 
>only a question of time that sooner or later a group of archaebacteria will
>be discovered that is closer to the eukaryotes than other archaebacteria 
>(and many will argue that the eocytes already fit this description).

Why do you say this? Have you forgotten already about "keeping an open
mind"?   (-:

Maybe it's only a question of time before we discover a group of
archaebacteria that are closer to the gram positive bacteria than other

>Yes, there are major distinction between pro- and eukaryotes; however, this
>should not lead one to overlook the major differences between archae- and

Unless, of course, those "major differences" are exaggerated.

>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.

[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.]

>[Following this discussion it might be news to some that not all genes 
>that encode enzymes involved in biosynthetic pathways and bioenergetics 
>group the archaebacterial homologues among their eubacterial counterparts.
>Examples that group the archaebacterial homologues as a distinct group 
>include ATPsynthases, cytochrome C oxidases, and argininosuccinate 

Yes, and it might also be news to some that not all genes required for
DNA replication, transcription, and translation group the archaebacteria
with eukaryotes. There are no simple solutions to this problem. It's 
best to reserve judgement until we have more and better data.

>The genes that group the archaebacteria among the eubacteria can be put 
>into two categories (often it is not clear which one of these, because 
>the rooting of the  respective phylogenies is controversial):   

>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. 

>or via an earlier eubacterial contributor to the eukaryotic cell (in my 
>opinion the latter alternative is still mainly based on wishful thinking).

Agreed. Notice that no one is suggesting that the genes involved in DNA
replication, transcription, and translation were transferred from an earlier
archaebacterial endosymbiont. Why not - is there a bias against such
suggestions?  (-:

>Category 2:  well resolved phylogenies that group the archaebacterial genes
>among the eubacteria. The longest internal branch connects all the 
>prokaryotes to all of the eukaryotes (e.g. HSP70). Midpoint rooting would 
>place the root in this longest internal branch.  I think that the best
>explanation for these phylogenies is horizontal transfer of genes from a
>eubacterium to the archaebacteria.

Alternatively, there could have been horizontal transfer of genes from a
primitive eukaryote to the archaebacteria. In other words, the "well
resolved phylogenies" could be correct and the problem genes are the ones
that show something different. Neither possibility can be proven at this
point so it is best to keep an open mind and not assume that archaebacteria
for a separate domain that clusters with eukaryotes.

It seems to me that your "best explanation" makes an assumption about the
"correct" phylogeny (namely an archaebacteria/eukaryote relationship).
Such assumptions are not justified at the present time.

>Assuming horizontal gene transfer, or the fusion of formerly 
>independent lines of descent, certainly complicates the interpretation of 
>molecular phylogenies.  However, given that some examples exist that 
>demonstrate cross-domin horizontal transfer, and that horizontal transfers
>and symbioses between extant organisms occur frequently, it seems strange 
>to assume that these events did not play an important role also in the 
>early evolution.

We would all prefer not to have to evoke horizontal gene transfer to explain
the data because it potentially calls into question all phylogenies. But
if we have to resort to this rationalization then let's make sure that
we do it in a way that best explains the data we have. This means that we
have to let the data generate the hypotheses and not assume a particular
hypothesis and try and twist the data to make it fit.

>If one looks at the data from a less "eukaryocentric" perspective 
>one recognizes that these processes also played an important role in the
>evolution of the other cellular lineages.

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.

>The finding of extensive horizontal gene transfer between eu- and 
>archaebacteria should not distract from the major horizontal transfer 
>(fusion) events associated with the emergence of the eukaryotes.

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

Larry Moran

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