DNA-DEPENDENT RNA-POLYMERASES AS PHYLOGENETIC MARKER MOLECULES

The large components of DNA-dependent RNA polymerases (RNAPs) of Archa ea, Bacteria and Eurarya were used as molecular markers for the recons truction of phylogenetic trees. Preferred phylogenetic trees of the th ree domains of organisms were determinded by a combination of the thre e major types of inference methods (pairwise distances, maximum parsim ony and maximum likelihood) applying the fuzzy logic data analysis met hod. The preferred phylogenetic trees for the Archaea and Bacteria sho w branching topologies which differ significantly from the topologies found using ribosomal RNAs as probes: the tree of the Archaea allows a unique location of a characteristics splitting event replacing the la rgest RNAP subunit (B) of the thermophilic sulfur archaea by two fragm ents (B' and B'') in methanogens and halophiles; the tree of the Bacte ria shows the lineage of the extreme thermophile Aquifex pyrophilus at a branching point located far away from the root of this domain - cle arly not supporting the hypothesis that hyperthermophilia is a relic o f primordial environmental conditions. The preferred branching topolog y of the universal phylogenetic tree reconstructed from the sequences of the second largest components (B) of the three eucaryal RNAPs (Pol I, Pol II and Pol III), the archaeal RNAP components B or B' plus B'', respectively, and the bacterial RNAP components, beta, confirmed the topology formerly inferred from another set of RNAP components: compon ents A of the eucaryal RNAPs, archaeal components A' plus A'', and bac terial beta' components. The preferred branching topology of this univ ersal tree is characterized by an internodal stretch separating the ar chaeal lineage and the lineage of the eucaryal Pols II and Pols III on the one hand, from the bacterial lineage and the lineage of the eucar yal Pols I on the other hand. The latter topology led us to the fusion hypothesis for the formation of the Eurcarya.