LIFES 3RD DOMAIN (ARCHAEA) - AN ESTABLISHED FACT OR AN ENDANGERED PARADIGM - A NEW PROPOSAL FOR CLASSIFICATION OF ORGANISMS BASED ON PROTEIN SEQUENCES AND CELL STRUCTURE

The three-domain proposal of Woese ef al. (Proc. Natl. Acad. Sci. USA 87, 4576 (1990)) divides all living organisms into three primary group s or domains named Archaea (or archaebacteria), Bacteria (or eubacteri a), and Eucarya (or eukaryotes), with Eucarya being relatives (or desc endants) of Archaea. Although this proposal is currently widely accept ed, sequence features and phylogenies derived from many highly conserv ed proteins are inconsistent with it and point to a close and specific relationship between archaebacteria and gram-positive bacteria, where as gram-negative bacteria are indicated to be phylogenetically distinc t. A closer relationship of archaebacteria to gram-positive bacteria i n comparison to gram-negative bacteria is generally seen for the major ity of the available gene/protein sequences. To account for these resu lts, and the fact that both archaebacteria and gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that t he primary division within prokaryotes is between Monoderm prokaryotes (surrounded by a single membrane) and Diderm prokaryotes (i.e., all t rue gram-negative bacteria containing both an inner cytoplasmic membra ne and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. Protein phyl ogenies and signature sequences also show that all eukaryotic cells ha ve received significant gene contributions from both an archaebacteriu m and a gramnegative eubacterium. Thus, the hypothesis that archaebact eria and eukaryotes shared a common ancestor exclusive of eubacteria, or that the ancestral eukaryotic cell directly descended from an archa ea, is erroneous. These results call into question the validity of the currently popular three-domain proposal and the assignment of a domai n status to archaebacteria. A new classification of organisms consiste nt with phenotype and macromolecular sequence data is proposed. (C) 19 98 Academic Press.