Thus,
21 genes are shared by these four distantly related bacteria.
Aquifex aeolicus are the most thermophilic bacteria, growing just below the boiling point of water. They are also thought to represent the earliest lineages to branch off the eubacterial tree.
Bacillus subtilis is a gram-positive soil bacterium that can use a wide variety of carbon sources. Very similar bacteria (
Clostridium) used to be thought most primitive.
Escherichia coli represent the gram-negative proteobacteria and live in the digestive tracts of many organisms. Their flagella are among the most studied.
Treponema pallidum is a spirochete whose flagellum is part of a rather specialized motility organelle known as the axial filament. As I mentioned, these four species are very distantly related, as seen by the phylogenetic tree constructed from 16s rRNA sequence (Fig 3). Furthermore, all four bacteria have experienced very different environmental pressures over the last several billions years. This strongly implies that these 21 genes were present in the last common ancestor of all eubacteria, thus comprising the Ur-IC flagellum. To further test this notion, I surveyed the flagellar genes of
Thermotoga maritima since
it is also a very deeply branching bacterium. According to the TIGR list of flagellar genes, everything in the Ur-IC list is represented, thus confirming what IC would predict.[7] Furthermore, this Ur-IC state has persisted for billions of years since it appeared. That billions of years of microbial evolution, in each lineage, have not imposed significant permutations on this IC core speaks to its true IC state.
Figure 3. Eubacterial phylogenetic tree. Adapted from [8]
Since the last detectable flagellum most likely contained these 21 genes (22, if we split FliG; 23 if we separate FliM and FliN), we can finally turn to the hypothesis of gradual CCAF to understand why it is so unconvincing.