Divergence of bacilli and the purple bacteria

PeterGogarten PeterGogarten
Tue Mar 15 10:51:49 EST 1994

In article <1994Mar7.194647.21672 at dal1> arlin at ac.dal.ca writes:
>In article <1994Mar1.181935.21441 at dal1>, aroger at ac.dal.ca relays comments
>from Peter Gogarten:
>>[ . . .]  The deepest branching eubacterium for which the ATPase
>> catalytic subunit sequence is known is Thermotoga maritima.  This sequence [....]
>I don't see how the general conclusion about "known groups of eubacteria"
>follows from the work described.  I thought Andrew was questioning the
>inter-phylum relationships on the 16S rRNA tree.  This is a reasonable
>skepticism because the links on the tree are short and bootstraps or other
>If the branching order of the 16S rRNA tree is not correct, then perhaps
>the node closest to {eukaryotes, archaebacteria} is not {thermotogales,
>other eubacteria} but {XXXX, other eubacteria} where XXXX might be
>planctomycetes, cyanobacteria, high-GC gram-positives or any of a dozen
>other eubacterial phyla.  Questioning the rRNA tree means questioning such
>matters.  If the root of duplicated protein trees falls between the nodes
>{eukaryotes, archaebacteria} and {thermotoga, {E.coli, B.subtilis}} this is
>not evidence that eubacteria are a clade or that Thermotoga is an outgroup
>to any eubacteria other than E.coli and B.subtilis.  Instead, eubacterial
>phylum XXXX might be an outgroup to all life.
>In short, if one doesn't use representatives of all eubacterial phyla in a

This is hard to do because it is not sure that all phyla are known yet, however, the ATPase data come pretty close to this requirement. 

>protein tree, then one is relying on the (questionable) 16S rRNA tree to
>inform one's judgment about which groups to include.  Such pruned protein
>trees will certainly be valuable in clarifying the relationships of the
>phyla *that are included in them,* but they leave open the possibility that
>"known groups of eubacteria" are paraphyletic, or if holophyletic, that
>thermophiles are not outgroups to other eubacteria.  And these issues are
>important for resolving questions about the history of thermophily and the
>status of the three 'urkingdoms.'

I am not sure that I grasp the meaning of your comment, may be I was not to clear in my posting.  Schleifer and Co-workers (from the TU Munich) did an extensive analysis of F-ATPase sequences, in my analyses I used about 15 different eubactaeria.  The sequences were analyzed at the DNA and at the protein level. The outgroup for the eubacteria is provided either by the noncatlytic F-ATPase subunits or by the vacuolar/archaebacterial ATPases (gives the same root).  So far the F-ATPase data are in agreement w
ith the 16S rRNA data, i.e., in both cases Thermotoga, green non sulfur bacteria, PS3 branch off before the cyanobacteria; and as I stated im my privious post, the deepest eubacterial branch branches off in a great distance from the outgroup.   Schleifer et al. have a paper in print in which they compare ATPase subunits, elongation factors and 16S rRNA phylogenies. In all cases similar or identical phylogenies between the different eubacterial phyla are obtained, in a seminar Schleifer claimed that the res
olution would be best for the 16S rRNA.  This does not prove that GC contents did not bias the data, the GC contents could even influence and bias the amino acid sequences (the results suggesting the monophyletic origin of plastids suggest that one should be very, very cautious), however, I think that this is not too likely to completely screw up the phylogenies.  For me a greater concern is that not all molecular data tell the same story.  The reason can be either unreliable or biased datasets, or the ste
p from molecular to species phylogeny is not as easy as sometimes assumed.  As I pointed out previously the ATPase subunit phylogenies point to at least two cases of horizontal gene transfer (one between an archaebacterium and an ancestor of Thermus and the Deinococci), the other between a eubacterium (close to the root of the gram positives) and a mesophilic archaebacterium.  I am not sure whether the horizontal gene transfers postulated based on other molecular phylogenies are due to the same events (the
n these might more resemble the fusion of formerly independent lineages) or whether these constitute many separate events in which only small portions of the genome were transferred (I suspect the former).  

I do not think that these different molecular phylogenies are due to ill resolved or biased data (the bootstrap probabilities for some of the data are pretty high, the different topologies when tested with protein and DNA maximum likelihood analyses are incompatible).  I think the paradigm of a tree to depict the species evolution is wrong. The 16S rRNA, ATPases and elongation factors suggest the phylogeny of one component of the organisms, glutamine synthases, heat shock protein homologues and glutamate d
ehydrogenases seem to reflect a different component.  Thus it appears (to me) that not only the eukaryotes resulted from the fusion of an archaebacterium like ancestor with a eubacterium like organism, at least a subgroup of the archaebacteria seems to have incorporated part (or all) of a eubacterial genome.

Peter Gogarten
Dept. Molecular and Cell Biology
University of Connecticut  

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