Archaebacteria and the Three Kingdoms

jrbrown at ac.dal.ca jrbrown at ac.dal.ca
Wed Apr 13 12:56:11 EST 1994

There are two major questions involved with the 
rooting and structure of the universal tree.  First, what 
is the level of support for the revelation of rRNA based 
phylogenetic analysis that the universal tree of life can 
be subdivided into archaebacterial, eubacterial and 
eukaryotic domains? Second, what is the true order of 
descent of archaebacteria, eubacteria and eukaryotes 
from the last common ancestral cell?  rRNA 
phylogenies do show the presence of three domains but 
do not support the notion that archaebacteria and 
eukaryotes are sister groups.  The only reliable way to 
root the universal tree is using ancient duplicated genes 
such as ATPase and Ef genes.  However, recent 
findings of archaebacterial-like V-type ATPase in 
eubacteria and F1-type ATPase in archaebacteria 
suggest that the full extent of the ATPase gene family 
has yet to be determined.  Furthermore, the elongation 
factor data set should be re-examined in the light of 
many more sequences being available since Iwabe's 
1989 analysis.  Finally, phylogenies based on other 
duplicated gene families need to be developed.  Garcfa-
Meza et al. (1994) have listed several candidate genes 
including lactate/malate dehydrogenases, LepA 
protein/initiation factor 2, superoxide dismutases, 
pyruvate oxidase/acetohydroxy acid synthetase, 
HisA/HisF, initiator/elongator met-tRNA and 
aminoacyl-tRNA synthetases.  In fact, we are obtaining 
new sequences and developing phylogenies for the 

I have made an earnest, but likely incomplete attempt, 
to collate all gene sequences which are readily alignable 
for all three domains.  Presently, I have found about 40 
types of genes which are represented by at least one 
species from each domain.  Based on this aggregate 
data, there is no statistical basis for saying that a 
majority of genes or the majority of genes in a 
particular metabolic or synthesis pathway support one 
tree topology over another.  (At this point, I digress to 
say that I would be interested in hearing about any 
findings about new, unpublished genes not previously 
detected in a particular domain). Many gene trees 
support the concept of three separate domains but there 
are a number of important exceptions such as glutamine 
synthetase, GDH, etc.  In summary, the rooting of the 
universal tree and the sanctity of the three domains are 
still open questions.  That's my two cents worth.


Garcfa-Meza, V., Gonzalez-Rodriguez, A., Lazcano. 
1994. Ancient paralogous duplications and the search 
of archean cells.  in G.R. Fleischaker, S. Colonna and 
P.L. Luisi (ed) Self-reproduction of supramolecular 
structures: From synthetic structures to models of 
minimal living systems. Kluwer, Amsterdam.

James R. Brown
Program in Evolutionary Biology
Canadian Institute for Advanced Research
Dept. of Biochemistry
Dalhousie University
Halifax, Nova Scotia
Canada B3H 4H7
(902) 494-3569
Internet: JRBROWN at ac.dal.ca

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