"James Lake and co-workers have lately proposed a radical re-structuring of the "universal" phylogenetic tree, to split Archaea into Halobacteria, Methanogens and Eocytes. This would mean there are three major groupings of prokaryotes (Eubacteria + Halobacteria, Methanogens and Eocytes), which could all constitute kingdoms on their own, given each is as unrelated to the others as any are to Eukarya."
picture of the tree is at
http://www.mcb.uct.ac.za/tutorial/unitree.gif
"The Eocyte Tree Makes Sense
A number of fundamental molecular properties have been thought to have an idiosyncratic distribution on the tree of life, principally because they did not fit the archael tree. Yet these same molecular properties fit the eocyte theory perfectly. This is particularly true for the organization of ribosomal rRNA operons.
Because small subunit ribosomal RNA sequences are the standard for defining the phylogenetic positions of organisms, a large data base of ribosomal RNAs exists and one knows far more about the organization of ribosomal operons than about any other operons. Eubacteria, halobacteria, methanogens, and eocytes contain three rRNAs, 16S, 23S, and 5S, which are homologous to the eukaryotic 18S, 5.8S+28S, and 5S. (For simplicity we will refer to both the eukaryotic and prokaryotic homologues using the prokaryotic labels.) The number of ribosomal rRNA transcriptional units varies between one and four in the halobacteria and the methanogens. Ribosomal operons are arranged in the same general pattern in eubacteria, halobacteria, and methanogens, namely 16S-tRNA-23S-5S. Occasionally an additional tRNA gene will be found between the 16S and 23S genes or following the 5S gene (reviewed in Brown, Daniels, & Reeve, 1989). Thermoplasma, which routinely clusters in phylogenetic trees with the methanogens, is an exception to this general rule and unlike any other prokaryote. Thermoplasma contains unlinked 16S, 23S and 5S genes (Tu & Zillig, 1982). The pattern in eocytes and eukaryotes is different from the eubacteria, halobacteria, and methanogens. In the eocytes, the 16S-23S genes are linked without a tRNA spacer and there is a variable linkage of 5S rRNA encoding genes to the 16S-23S unit. The non-operon-associated 5S rRNA gene of D. mobilis forms its own transcriptional unit (Kjems & Garrett, 1988), but those of many other eocytes contain a 16S-23S-5S transcriptional unit. The eukaryotic pattern is similar with a 16S-23S (equivalent) transcription unit lacking tRNA spacers and with the 5S either separately transcribed or linked (Gerbi, 1985). An exception to this rule is found among the Cryptomonads where the rRNA genes are unlinked (Gray, 1992).
Although it can not be easily explained by the archaebacterial theory, this pattern of rRNA operon organization fits the eocyte tree well. [Click to see the tree.] Only a single change of operon type is required to accommodate this distribution on the eocyte tree. Namely, the 16S-tRNA-23S-5S pattern found in eubacteria, halobacteria, and methanogens is substituted by the derived 16S-23S type at the position on the tree shown by the box. Depending upon the operon organization in Methanopyrus (presently unknown), the site of the box will be either before or after Methanopyrus branches. In either case, only a single change will be required. The archael tree, does not explain this distribution, unless one postulates multiple independent creations of operon types. Since ribosomal operon organization is generally regared as being a slowly evolving character, this again lends considerable support to the eocyte theory.
The Universal Tree of Life
Because of the long branch attraction artifacts, we searched for molecular sequences which contained structural features, such as inserted segments. Since the insertion of segments happens much less frequently than individual nucleotide changes, they are much less sensitive to long branch artifacts, and can, therefore, be more easily interpreted.
The molecule we chose to study was protein synthesis elongation factor EF-Tu (EF-1 in eukaryotes), (Rivera & Lake, 1992). EF-Tu is an ubiquitous protein that transports aminoacyl-tRNAs to the ribosome and participates in their selection by the ribosome. Within the GDP-binding domain of EF-Tu, the amino acid sequence, KNMITG 94 , which is strictly conserved in EF-1 and EF-Tu sequences, terminates an -helix and is followed by a -strand that is terminated by GPMP 113 at the GDP binding site. The sequence QTREH 118 then starts a 3 10 helix. The amino acid motifs of the eukaryotic EF-1 are similar, except that the four-amino acid sequence GPMP 113 in prokaryotes is replaced by the 11-amino acid sequence GEFEAGISKDG, and its variants, in eukaryotes, as shown below.
Taxon Organism Left
Sequence 11 a. a.
Segment 4 a. a.
Segment Right
Sequence
Eukaryotes Human KNMITG TSQADCAVLIVAAGV GEFEAGISKNG QTREH
" Tomato KNMITG TSQADCAVLIIDSTT GGFEAGISKDG QTREH
" Yeast KNMITG TSQADCAILIIAGGV GEFEAGISKDG QTREH
Eocytes P.occu. KNMITG ASQADAAILVVSARK GEFEAGMSAEG QTREH
" D.muco. KNMITG ASQADAAILVVSARK GEFEAGMSAEG QTREH
" A.infe. KNMITG ASQADAAIIAVSAKK GEFEAGMSEEG QTREH
" Su.sol. KNMITG ASQADAAILVVSAKK GEYEAGMSAEG QTREH
Methanogens T.celer KNMITG ASQADAAVLVVAVTD ---GVMP QTKEH
& Relatives Mc.van. KNMITG ASQADAAVLVVNVDD AKSGIQP QTREH
Halobacteria H.maris KNMITG ASQADNAVLVVAADD ---GVQP QTQEH
Eubacteria Tt.mar. KNMITG AAQMDGAILVVAATD ---GPMP QTREH
" S.plat. KNMITG AAQMDGAILVVSAAD ---GPMP QTREH
" Mitoch. KNMITG AAQMDGAIIVVAATD ---GQMP QTREH
Since the eukaryotic 11 amino acid insert is so well conserved among eukaryotic sequences we thought that eocyte sequences might also contain the 11 amino acid insert. Using the polymerase chain reaction and DNA primers designed for use with the KNMITG and QTREH sites, we amplified, cloned, and sequenced the insert region. The eocyte amino acid sequences, translated from DNA, shared the eukaryotic motif (11 amino acids) rather than that found in methanogens, halobacteria, and eubacteria (4 amino acids). The longer 11-amino acid segment, present in eocytes and eukaryotes, shares little similarity with the shorter, four-amino acid segment found in other prokaryotes.
Based on these results, we could directly test the eocyte and archael theories for the origin of the nucleus. [Click on the trees to the left to get a higher resolution image.] The fundamental difference between these two theories is that in the eocyte tree (at the top of the figure) the eukaryotic nucleus shares a most recent common ancestor solely with the eocytes, whereas in the archaebacterial theory eocytes are no closer to eukaryotes than are methanogens or halobacteria, since they are all included within archae.
We have mapped the changes onto the trees representative of both theories. Starting from the four amino insert at the root of the tree, each solid box indicates a change from the four-amino acid segment to the 11-amino acid form. The eocyte tree is favored because it requires only a single change, whereas the archaebacterial tree requires two independent but identical changes. (The archael tree could also be explained by one appearance of the 11-amino acid form and one reappearance of the 4-amino acid form, but even so, two changes would be required.)
Several lines of reasoning buttress the interpretation that eocytes are the closest relatives of the eukaryotes. First, the 11-amino acid segments present in eocytes and eukaryotes are very likely homologous. Eight of eleven amino acids (seven in Sulfolobus and Acidianus) are identical to the consensus eukaryotic sequence. Amino acid shuffling of the segments produced random alignments that score 6-7 standard deviations lower than those found for the eukaryotic-eocyte alignment, thereby implying homology (Waterman & Eggert, 1987). Second, the alignments are well defined. No gaps are needed to align the eukaryotic and eocytic EF-1 sequences, and no gaps are needed to align the eubacteria, methanogen, and halobacterial sequences. Third, the sequences encoding EF-1 are not likely to have been laterally transferred between organisms, since EF-1 is present in all cells and, during protein synthesis, interacts with cellular components encoded by genes dispersed throughout the bacterial genome, including aminoacyl-tRNAs, ribosomal proteins, elongation factor EF-Ts, and 16S and 18S ribosomal RNAs. These results lend strong support to the proposal that the eukaryotes and eocytes are sister taxa within the tree of life.
Recent Analyses Show the Eocyte Tree to be Correct
Perhaps the most satisfying support for the eocyte theory has come from sequence analyses of EF-1 genes to reconstruct the tree of life. This is paraticularly true in the last several years, as more sophisticated tree reconstruction algorithms have been developed, and as new methods have been devised to correct for the variation of evolutionary rates at different nucleotide positions within a sequence. During the 1990's, many analyses of EF-1 , as well as EF-G and 16/18S rRNAs, have supported the eocyte tree, in contrast to the situation in the late 1980's. A representation of the results obtained can be seen by clicking here. In support of the eocyte theory, virtually every recent analysis of EF-1 sequence has supported the eocyte theory and rejected the archael theory.
Conclusions
Of all the genes functioning in translation that have been sequenced to date, the EF-Tu molecule seems to offer the most reliable indication of early divergences. Genome analyses show it is the slowest evolving sequence of its class and should, therefore, be the most reliable for phylogenetic purposes. It is also unlikely to be laterally transferred between organisms because it is present in all cells and, during protein synthesis, interacts with cellular components that are dispersed throughout the bacterial genome. Furthermore, direct phylogenetic analyses of this molecule by almost all authors support the eocyte tree. Significant support for the eocyte tree also comes from the observations that eukaryotic ribosomal operons are organized like those of Sulfolobus, Desulfurococcus, and Thermoproteus and not organized like the tRNA containing rRNA operons of halobacteria, methanogens, and eubacteria."
9-13-2000
http://genomics.ucla.edu/eocyte
I have no better up-to-date information on the rooting of the tree of life and the LUCA than this. Do you have more up-to-date information? Sharing?