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Archaebacteria and the Three Kingdoms

L.A. Moran lamoran at gpu.utcc.utoronto.ca
Sun Apr 10 18:42:47 EST 1994

We are discussing whether Archaebacteria form a separate domain that may,
or may not be, monophyletic. I have also raised questions about whether
the Archaebacteria are more closely related to eukaryotes. My position is
that the data is not clear on these points and that it is not appropriate
to elevate Woese's classification to the status of "theory" or "law" or
(ugh) "paradigm". It should be referred to as a working hypothesis with 
much contrary evidence. The debate has very real significance for me since 
I write textbooks. What should we say in the textbooks about the Three Domain

J.Peter Gogarten (Gogarten at uconnvm.uconn.edu) writes,

     "There are many characters (not only 16S rRNAs) which separate Archae-
      and Eubacteria (see Zillig et al., 1992, for a listing). With many
      molecular markers the Archaebacteria appear closer to the Eukaryotes
      (e.g.: ATPases, elongation factors, RNA polymerases). Not all of these
      molecular markers show the Archaebacteria as a monophyletic group,
      in some analyses they appear paraphyletic; however, the branch that
      separates the two archaebacterial groups is very short (as is the 
      branch that connects the 16S rRNA of the Archaebacteria to the other

There are also a great many characters that unite archaebacteria and
eubacteria and distinguish them from eukaryotes (eg. genome organization,
lack of nuclear membrane, cell wall, no ER, single RNA polymerase, flagella,
no histones, no 5.8S RNA, operons, no actin or tubulin, signal recognition
particle sequence). I have not read the Zillig et al. paper but I'll try to
find a copy.

Dendrograms constructed by comparing the sequences of elongation factors are
not very reliable. Many of the published alignments can be improved easily.
Lake (1991) has pointed out that the alignments of these sequences depend
on the order of the alignment and that several different dendrograms can be
generated. However, visual inspection of the EF-Tu sequences does suggest
that the eukaryotic genes are more closely related to archaebacteria. 

The alignment of RNA polymerase subunit sequences is also difficult. The 
amino acid sequences of the largest subunit appear to support a relationship
between archaebacteria and eukaryotes but the dendrogram constructed from
sequences of the second largest subunit do not (Iwabe et al. 1991).

I am confused about the ATPases. Perhaps Peter Gogarten can help to explain
a few things since he has analyzed these genes. If I understand things 
correctly then the eukaryotic subunits of the F-ATPases are all derived
from mitochondria and chloroplasts. Thus they are of no use in deciphering
the origins of archaebacteria and eukaryotes. Is this correct? The 
eukaryotic V-ATPases, on the other hand, are not found in mitochondria
or chloroplasts. Thus the genes are presumed to have been present in the
ancestral eukaryote. The eukaryotic V-ATPase subunit genes are much
more closely related to the archaebacterial genes than to eubacterial 
genes. Right?

I have had trouble finding alignments of these proteins in order to see 
for myself how good they are. Perhaps there are aligments in one of the 
papers that I have not been able to find (ie. your Z. Naturforsch paper). 
The Miyata et al. (1991) alignments are useless to me because, as is usual 
with this group, only selected regions of the proteins are analyzed - gaps 
are ignored. In the Gogarten et al. (1989) paper it seems that only a short 
stretch of 200 amino acid was used to construct the dendrogram. Is this 
because the rest of the sequence couldn't be aligned?

All of the dendrograms indicate very large distances between the Eubacteria
and the Archaebacteria/Eukaryotes (ie. V-ATPases and F-ATPases). Also the
similarity between the catalytic and non-catalytic subunits must be very low
- what is it in terms of percent identity? If we were to attach a time scale 
to the published dendrograms it looks like the Eubacteria vs. Archae-
bacteria/Eukaryote (V-ATPase and F-ATPase) split took place about five billion
years ago and the catalytic vs. non-catalytic split is even earlier. This 
suggests that there is something strange about the evolution of these genes.

Benachenbou-Lahfa et al. (1993) have been critical of the EF-Tu and ATPase
data. They point out that their glutamate dehydrogenase dendrograms do
not support the Three Domain hypothesis. How do you respond to their
criticism of your results and to Sidow and Bowman (1991) who claim that
your methodology was flawed? This is an ideal forum to continue this debate
and to refute your critics. (You may have done this in Hilario and Gogarten
(1993) - I can't find this paper; but I haven't given up yet.)

J.Peter Gogarten (Gogarten at uconnvm.uconn.edu) writes,

     "Based only on nucleotide data it will be difficult to discriminate 
      between the para and monophyletic origin of the archaebacteria.  
      Rivera and Lake report a higher order character (a deletion/insertion)
      that unites only some of the archaebacteria with the eukaryotes."

I agree that the data is not good enough. You pointed this out in your 
rebuttal to Lake (Linkkila and Gogarten, 1991). Hasegawa et al. (1993)
now claim that their EF-Tu/EF-1alpha data does not show the archaebacteria
as a monophyletic group - but the archae are still more closely related
to eukaryotes. Miyata et al. (1991) show that the archaebacteria are 
paraphyletic based on the ATPase tree. The ATPase tree has Sulfolobus
(eocyte) more distantly related to the eukarotes while the EF-Tu tree
has this species possibly branching with the eukaryotes. They can't
both be correct.

However, let's not get distracted from the main point. Whether the archae-
bacteria form a paraphyletic or monophyletic group is less important than
whether they form a "group" at all or whether they are more closely related
to eukaryotes than to other bacteria.

Let me close with a quotation from Benachenhou-Lahfa et al. (1993) that
will hopefully stimulate more traffic in this thread.

     "Taken as a whole, these data suggest that recent affirmations
      about branching of archaebacteria must be taken with great caution.
      Indeed, after publication of the resuts of Gogarten et al. (1989)
      and Iwabe et al. (1989) and their theoretical endorsement by Woese
      et al. (1990), it was taken for granted that the root of the 
      universal tree was positioned within the eubacterial line of
      descent, suggesting that archaebacteria and eukaryotes were 
      clustered and that archaebacteria were monophyletic...

      Recently, Sidow and Bowman (1992) have pointed out in an opinion
      paper that the data of Gogarten et al. (1989) and Iwabe et al.
      (1989), although conceptually very interesting, could not be
      regarded as definitive since in both cases the methodology used
      to establish the trees could be criticized. Moreover, new protein
      sequences and new multiple alignments appeared (Tsutumi et al.
      1991; Creti et al. 1991), which, in our opinion (Forterre et al.
      1992), challenged the resulats of both Gogarten et al. (1989) and
      Iwabe et al. (1989), suggesting that both ATPases and elongation
      factors may not be such good choices to root the tree of life."

Laurence A. Moran (Larry)

Benachenhou-Lahfa, N., Forterre, P. and Lebedan, B. (1993) Evolution of
   glutamate dehydrogenase genes: evidence for two parologous protein
   families and unusual branching patterns of the archaebacteria in the
   universal tree of life. J. Mol. Evol. 36, 335-346.

Gogarten, J.P., Kibak, H., Dittrich, P., Taiz, L., Bowman, E.J., Bowman, B.J.,
   Manolson, M.F., Poole, R.J., Date, T., Oshima, T., Konishi, J., Denda, K.,
   and Yoshida, M. (1989) Evolution of the vacuolar H+ - ATPase: Implications 
   for the origin of eukaryotes. Proc. Natl. Acad. Sci. (USA) 86, 6661-6665.

Hasegawa, M., Hashimoto, T., Adachi, J., Iwabe, N. and Miyata T. (1993)
   Early branchings in the evolution of eukaryotes: ancient divergence
   of Entamoeba that lacks mitochondria revealed by protein sequence
   data. J. Molec. Evol. 36, 380-388.

Hilario, E., Gogarten, J.P. (1993) Horizontal Transfer of ATPase Genes -The
   Tree of Life becomes a Net of Life. BioSystems 31, 111-119

Iwabe, N. t al. (1991) Evolution of RNA polymerases and branching patterns
   of the three major groups of archaebacteria. J. Mol. Evol. 32, 70-78.

Lake, J. A. (1991) The order of alignment can bias the selection of tree
   topology. Mol Biol. Evol. 8, 378-385.

Linkkila, T.P. and Gogarten, J.P. (1991) Tracing origins with molecular
   sequences: rooting the universal tree of life. TIBS 16, 287-288.

Miyata, T. et al. (1991) Evolution of Archaebacteria: phylogenetic 
   relationships among archaebacteria, eubacteria, and eukaryotes.
   in EVOLUTION OF LIFE, S. Osawa and T. Honjo eds. Springer-Verlag
   pp. 337-351.

Sidow, A. and Bowman, B.H. (1991) Molecular phylogeny. 
   Curr. opin. Gene Dev. 1, 451-456.

Zillig W, Palm P, Klenk H-P (1992) A model of the early evolution
of organisms: The arisal of the three domains of life from the common
ancestor. In: H Hartman, K Matsuno (eds) The origin and evolution of the
cell (World Scientific, Singapore, New Jersey, London, Hong Kong) pp.

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