Origin of the Nucleus


EMs of Large and Small Ribosomal Subunits

    In the early days of the search for the prokaryotic ancestor of eukaryotes, graduate student rotations in our lab would focus on isolating ribosomes from unusual organisms. After Carl Woese reported data suggesting that the 16S ribosomal RNA (rRNA) of methanogens was different in sequence from those of most prokaryotes (ref. woese and fox), we quickly elucidated that methanogens, indeed, had ribosome structures with significant differences from those of eukaryotes and most other prokaryotes (ref, 1982). At that time, novel hyperthermophilic organisms were being discovered primarily by Wolfram Zillig and Karl Stetter in Germany. We were astonished to find that several of these contained structural features that had previously only been observed in eukaryotic ribosomes (Science, 1983).

    Electron micrographs of both the large and small subunits are shown in the accompanying figure. Gradually we became aware that different ribosome structures were characteristic of methanogens, still different were characteristic of halobacteria, and still others were characteristic of the newly discovered eocyte hyperthermophiles.

    For more detailed electron micrographs of large and small subunits of eocyte ribsomes click on the image to the left.



    At that time, Walter Fitch, was on sabbatical at UCLA and explained the methods of cladistics and how we could use the various ribosomal structures in order to determine a tree of life. The results of that first analsis were published in PNAS (xxx, 1983).

    Later, similar results were obtained using the automated methods of image analysis developed by J. Frank. The average structures of E. coli (eubacteria), Methanococcus (methanogen), Sulfolobus (eocyte), and Saccharomyces (eukaryote) small ribosomal subunits are shown to the left. Each image represents the "average" of several hundred electron micrographs.

    Click on the image to the left for more detail.
Average Structures for Ribosomes from Eubacteria, Methanogen, Eocyte, and Eukaryote.
Archaeal versus Eocyte Tree.

    Our analysis of ribosome structure showed a tree of life whose topology places eocytes closest to the eukaryotes. This finding caused a stir because it showed that the archaebacteria were a diverse (non-monophyletic) group and that only one part of the group, namely the eocytes, was closest to the eukaryotes.

    The unrooted evolutionary tree that best fits the ribosomes' structural differences can be seen to the left.



    In the early 80's, when ribosome structure was indicating that eocytes were the closest prokaryotic relatives to eukaryotes, one finding was suggesting that the picture might not be so simple. The lipids found in eukaryotes did not fit the evolutionary pattern so nicely. The eubacteria contain primarily ester lipids, whereas halobacteria, methanogens, and eocytes contain ether lipids, and eukaryotes contain primarily ester lipids (and some ether lipids). This suggested that eukaryotes might have obtained their membranes from eubacteria, and their translation apparatus from eocytes. Because of this inconsistency and because of the fact that the nucleus, like the chloroplast and mitochondrial endosymbionts, is surrounded by a double membrane, we proposed the endokaryotic hypothesis, shown below. According to this view, the nucleus may be an endosymbiont captured by an eubacterial host. New data from whole genome analyses (discussed later) are, in fact, supporting this early proposal.

Karyogenic versus Endokaryotic Hypothesis

Home Introduction The Diversity of Life Ribosome Structure Origin of the Nucleus Sequence Analysis Universal Tree of Life Support for Eocyte Tree The Eocyte Tree Makes Sense Conclusions