NUCLEIC ACID ANALYSIS AND THE ENDOSYMBIOTIC HYPOTHESIS
Authors: Phillips D. O. , Carr N. G. 
Published: April 2006

It is generally agreed that the first organisms were prokaryotic in nature. However, opinions differ as to the mechanism responsible for the origin of the eukaryotic cell – whether it arose by direct filiation from an ancestral blue‐green alga or by a series of symbioses.

The timing of the emergence of photosynthesis in eukaryotes has largely been based on evidence from Precambrian palaeontology. For this reason attention is drawn to recent reassessments of the Precambrian fossil record, which have suggested that a number of structures previously considered to be remnants of eukaryotic nuclei and organelles may instead have been artifacts that formed in certain blue‐green algae during their lithification.

Evidence regarding the mechanism responsible for the origin of chloroplasts may be sought in the molecular fossil record. Studies employing the techniques of DNA‐RNA hybridization and RNA sequencing (oligonucleotide cataloguing) have established the prokaryotic nature of chloroplast ribosomal RNAs. In addition, a close phylogenetic relationship between the blue‐green algaAphanocapsa6308 and the chloroplasts ofEuglena gracilishas been indicated. By contrast, the sequence resemblance of prokaryotic and chloroplast 16 S rRNAs to eukaryotic 18 S rRNAs is revealed to be no greater than that expected between completely unrelated molecules. However, the size differences which exist between 16 S and 18 S rRNAs raise doubts as to whether these RNA species are in fact directly comparable. On the other hand, all known examples of mature 5 S rRNA are approximately 120 nucleotides in length, and thus this RNA would appear to bridge the evolutionary discontinuity between prokaryotes and eukaryotes in an almost unambiguous manner. The identification of 5 S rRNA in chloroplast ribosomes has therefore prompted a number of investigations designed to establish the prokaryotic or eukaryotic affinities of this RNA species. These have confirmed the prokaryotic nature of chloroplast 5 S rRNAs, and have indicated the sequence dissimilarity of these species to the cytoplasmic 5 S rRNAs of eukaryotes. However, it is pointed out that such results can only provide conclusive support for the endosymbiotic hypothesis, if rates of change in homologous RNAs have remained approximately constant in all lines.

Combined evidence suggests that nucleotide substitutions in cytoplasmic ribosomal RNAs have occurred more frequently during the evolution of flowering plants, Gramineae in particular, than during the evolution of yeast or vertebrates. By contrast, chloroplast ribosomal RNAs are shown to be very strongly conserved. Moreover, considerable disparities are also noted in the relative amounts of change in prokaryotic and eukaryotic 5 S rRNAs. Although undoubtedly associated with their different architectures and functional roles, it is suggested that the primary explanation for this phenomenon lies in the fact that the cytoplasmic 5 S rRNAs of eukaryotes are not derived from that of the protoeukaryote host, but rather, from that of the protomitochondrion. The cytoplasmic j.8 rRNAs are now considered to be the extant descendants of the original protoeukaryote 5 S rRNA these species having increased in size in a similar manner to the other cytoplasmic ribosomal RNAs of eukaryotes.

Because the rates of nucleotide substitution in homologous prokaryotic and eukaryotic ribosomal RNAs are non‐identical, consideration is given to derived character states. The late methylated sequence ‐Gm26Am26AC– has been identified in the 16 S rRNAs of many prokaryotic microorganisms and may possibly be universal in the 18 S rRNAs of eukaryotes. Although its presence has been indicated in the 18 S rRNA ofEuglena gracilis, it is absent from the chloroplast 16 S rRNA of this protist, as well as from the 16 S rRNAs ofAphanocapsa6308 and many other blue‐green algae. Direct filiation would seem unable to provide a satisfactory explanation for this phenomenon. As a result it ii included that chloroplasts, and most probably mitochondria also, are of endosymbiotic origin.