According to myself investigations based on the analysis of the percentage of the genes shared by different bacterial clades, closest clade to Archaea is Actinobacteria and for Bacillus closest one of course Clostridia but on the second place we can see again Actinobacteria. So it is quite possible that Actinobacteria, Neomura and Bacillus had the common ancestor. But based on the analysis of the genes reading directions distributions inside bacterial genomes I guess that this common ancestor was close to Clostridia clade. LUCA probably had RNA-based chromosome which in the secondary structure was organized as one huge stem. So during transcription process ribosome can move only one way. As consequence all genes had the same reading direction. Afterwards when RNA-based genome was transformed to DNA-based genome each part of the RNA steam secondary structure complemented by the second chain was converted to the half of the new circular chromosome ring. So as result all genes in the one half of the chromosome had one direction and all (initially the same) genes on it other part had an opposite direction. If this hypothesis have sense than the clade which is closer to the root should still have large degree of asymmetry in the genes directions in the two parts of the ring. And this is exactly what we can see in the Clostridia clade. Per example Acetohalobium arabaticum had more than 90% of genes which is oriented in the same direction in the each part of the chromosome. It is absolutely statistically impossible to have this distribution after the just by chance process. So based on this method I am estimate that most antic clade is Clostridia. But Bacillus, Actinobacteria and Fusobacteria also old enough. Archaea probably much younger. This hypothesis can also explain why operons so widely distributed inside Firmucutes (probably most protein complexes in LUCA genome worked on the base of the self-assembling like per example in the the present tense bacteriophages).
I am particularly agree with the author in some points.
2 December 2010
According to myself investigations based on the analysis of the percentage of the genes shared by different bacterial clades, closest clade to Archaea is Actinobacteria and for Bacillus closest one of course Clostridia but on the second place we can see again Actinobacteria. So it is quite possible that Actinobacteria, Neomura and Bacillus had the common ancestor. But based on the analysis of the genes reading directions distributions inside bacterial genomes I guess that this common ancestor was close to Clostridia clade. LUCA probably had RNA-based chromosome which in the secondary structure was organized as one huge stem. So during transcription process ribosome can move only one way. As consequence all genes had the same reading direction. Afterwards when RNA-based genome was transformed to DNA-based genome each part of the RNA steam secondary structure complemented by the second chain was converted to the half of the new circular chromosome ring. So as result all genes in the one half of the chromosome had one direction and all (initially the same) genes on it other part had an opposite direction. If this hypothesis have sense than the clade which is closer to the root should still have large degree of asymmetry in the genes directions in the two parts of the ring. And this is exactly what we can see in the Clostridia clade. Per example Acetohalobium arabaticum had more than 90% of genes which is oriented in the same direction in the each part of the chromosome. It is absolutely statistically impossible to have this distribution after the just by chance process. So based on this method I am estimate that most antic clade is Clostridia. But Bacillus, Actinobacteria and Fusobacteria also old enough. Archaea probably much younger.
This hypothesis can also explain why operons so widely distributed inside Firmucutes (probably most protein complexes in LUCA genome worked on the base of the self-assembling like per example in the the present tense bacteriophages).
Competing interests
None declared