PROTEIN PHYLOGENIES AND SIGNATURE SEQUENCES - EVOLUTIONARY RELATIONSHIPS WITHIN PROKARYOTES AND BETWEEN PROKARYOTES AND EUKARYOTES

The evolutionary relationships within prokaryotes and between prokaryo tes and eukaryotes is examined based on protein sequence data. Phyloge nies and common signature sequences in some of the most conserved prot eins point to a close evolutionary relationship between Archaebacteria and Gram-positive bacteria. The monophyletic nature and distinctness of the Archaebacterial domain is not supported by many of the phylogen ies. Within Gram-negative bacteria, cyanobacteria are indicated as the deepest branching lineage, and a clade consisting of Archaebacteria, Gram-positive bacteria and cyanobacteria is supported by signature seq uences in many proteins. However, the division within the prokaryotic species, viz. Archaebacteria <-> Gram-positive bacteria --> Cyanobacte ria --> other groups of Gram-negative bacteria, is indicated to be not very rigid but, Instead is an evolutionary continuum. It is expected that certain species will be found which represent intermediates in th e above transitions. By contrast to the evolutionary relationships wit hin prokaryotes, the eukaryotic species, which are structurally very d ifferent, appear to have originated by a very different mechanism. Pro tein phylogenies and signature sequences provide evidence that the euk aryotic nuclear genome is a chimera which has received major contribut ions from both an Archaebacterium and a Gram-negative bacterium. To ex plain these observations, it is suggested that the ancestral eukaryoti c cell arose by a symbiotic fusion event between the above parents and that this fusion event led to the origin of both nucleus and endoplas mic reticulum. The monophyletic nature of all extant eukaryotic specie s further suggests that a 'successful primary fusion' between the prok aryotic species that gave rise to the ancestral eukaryotic cell took p lace only once in the history of this planet.