Archaebacteria Then … Archaes Now (Are There Really No Archaeal Pathogens?)

In 1977, Carl Woese and George Fox argued that although methanogens looked like bacteria, they had very different cell wall structures and unique methanogenesis-related coenzymes and RNase T1 digestion of methanogen 16S rRNAs generated oligonucleotides so different from those from bacterial 16S rRNAs and from eukaryotic 18S rRNAs that methanogens should be placed in a third phylogenetic urkingdom, the Archaebacteria (81). They conceded that “almost nothing is known regarding their molecular biology” but concluded that “there is no reason at present to consider methanogens as any closer to eubacteria than to the cytoplasmic component of the eukaryote.” This started a scientific debate that has continued with unabated vigor for over 20 years. In 1977, methanogens were the only Archaebacteria, and not many more were predicted (81), but by 1980 the archaebacterial urkingdom had already grown to include halophiles and thermoacidophiles, and the presence of an RNA polymerase with a complex subunit configuration similar to eukaryotic RNA polymerases had been added to the list of definitive archaebacterial features (29). The 16S rRNA sequence data were by then presented in the now familiar phylogenetic tree format, and the three urkingdoms were shown arising independently from a common, less complex ancestor designated the progenote. It was tempting to comment here on the past and present arguments for and against the urkingdom concept, the number of urkingdoms, the branching relationships in the 16S rRNA phylogenetic tree, and the nature of the progenote, the universal and last common ancestors of all life (6, 9, 30, 32, 39, 49, 50, 54, 78, 81–83). But instead, from my perspective it seemed more appropriate to review how the revolutionary/heretical archaebacterial proposal has been investigated experimentally. What has been done, what were the driving forces for the research undertaken, what do we know now, what have complete archaeal genome sequences contributed, and what’s next?