13.5 Transcription in Archaea Is More Similar to Transcription in Eukaryotes Than to Transcription in Eubacteria

Some 2 billion to 3 billion years ago, life diverged into three lines of evolutionary descent: the eubacteria, the archaea, and the eukaryotes (see Chapter 2). Although eubacteria and archaea are superficially similar—both are unicellular and lack a nucleus−the results of studies of their DNA sequences and other biochemical properties indicate that they are as distantly related to each other as they are to eukaryotes. The evolutionary distinction between archaea, eubacteria, and eukaryotes is clear. However, did eukaryotes first diverge from an ancestral prokaryote, with the later separation of prokaryotes into eubacteria and archaea, or did the archaea and the eubacteria split first, with the eukaryotes later evolving from one of these groups?

Studies of transcription in eubacteria, archaea, and eukaryotes have yielded important findings about the evolutionary relationships of these organisms. Archaea, like eubacteria, have a single RNA polymerase, but this enzyme is most similar to the RNA polymerases of eukaryotes. As discussed earlier, bacterial RNA polymerase consists of 5 subunits, whereas eukaryotic RNA polymerases are much more complex; for example, RNA polymerase II is composed of 12 subunits. Archaeal RNA polymerase is similarly complex, with 11 or more subunits. Furthermore, the amino acid sequence of RNA polymerase in archaea is similar to the amino acid sequence of eukaryotic RNA polymerase II.

Archaeal promoters contain a consensus sequence similar to the TATA box found in eukaryotic promoters. The archaeal TATA box is found approximately 27 bp upstream of the transcription start site and, as in eukaryotes, helps to determine the location of the transcription start site. Archaea possess a TATA-binding protein (TBP), which is a critical transcription factor found in all three of the eukaryotic polymerases but not in eubacterial RNA polymerase. TBP binds the TATA box in archaea with the help of another transcription factor, TFIIB, which also is found in eukaryotes but not in eubacteria. However, some other regulators of transcription found in archaea are more similar to those found in bacteria, emphasizing that transcription in archaea is not entirely eukaryotic in nature. As prokaryotes, archaea lack a nuclear membrane, but many species do produce histone proteins, which help compact the DNA and form nucleosome-related structures.

Thus, transcription, one of the most basic of life processes, has strong similarities in eukaryotes and archaea, suggesting that these two groups are more closely related to each other than either is to the eubacteria. This conclusion is supported by other data, including those obtained from a comparison of gene sequences.