In the course of the ribosomal-RNA studies another unexpected archaebacterial property emerged, one that was to provide the first clue to the significance of the differences between archaebacteria and true bacteria. Central to the process of translation is the transfer RNA molecule. It recognizes a three base "codon" in messenger RNA specifying a particular amino acid, and it delivers that amino acid to be incorporated into the protein chain. A number of the nucleotides in a transfer-RNA molecule are modified, that is, their structure is altered chemically after they have been incorporated into the molecule; most often a methyl group is added to the nucleotide at some position on either the base or the sugar. Biologists had come to believe one particular modification was characteristic of a certain position in almost all transfer-RNA molecules in almost all organisms: at that position the base uracil has been methylated to form thymine (which is normally present only in DNA, not in RNA). It turns out that all transfer RNA's of all archaebacteria lack this thymine unit; instead the uracil has been modified in one of two other ways to yield a pseudouridine or an as yet un identified nucleotide.
If one compares both ribosomal RNA and transfer RNA in eukaryotes, eubacteria and archaebacteria, one finds a general pattern, of which the replacement of thymine in archaebacterial transfer RNA's is only one example. The same regions in the RNA's tend to be modified in all three primary lines of descent, but the nature of the modification tends to vary from one kingdom to another. The differences are of two kinds. Either the modification of a given base is different in each of the kingdoms, or a given base is modified in one kingdom and in another kingdom the modification is made to an adjacent base. These modes of variation suggest that the modifications have evolved separately in each major line of descent.