Given that the archaeal RNA polymerase is needlessly complex when compared with the eubacterial RNA polymerase, let’s take a closer look.
The bacterial RNAP contains four subunits, the yeast RNAP contains 12 subunits, and the archaeal RNAP contains 11 subunits. So when it comes to complexity (the number of parts), we would group the archaeal and eukaryotic versions together.
Yet when it comes to size (HT to Guts), the archaeal and bacterial version group together, both being around 400 kD. In contrast, the yeast RNAP is around 600 kD. So we do see evidence of streamlining in archaea – it’s simply in the size and not the complexity of the RNAP. And this makes the needless complexity of the archaeal RNAP even more perplexing.
The bacterial RNAP does not contain any subunits that are specific to bacteria, meaning their four subunits are universal. In yeast, these are known as Rpb1, 2, 3, and 11 and it is known these four comprise the assembly and catalytic core of this machine.
This then means that the yeast RNAP contains 8 subunits that are not found in bacteria. And of these eight subunits, six of them (RNAP 4, 5, 7, 10, 11, and 12) are homologous to the archaeal RNAP. Do these subunits also interact in a similar fashion? Yes, as here is a schematic of their respective interaction network (where homologous subunits are coded with the same color):
Holy smokes, it’s looking more and more like the archaeal RNAP is a miniaturized version of the eukaryotic RNAP. The major difference is that the eukaryotic RNAP has two components not seen in the archaeal version – Rpb 8 and 9. But wait!
Early evolution of eukaryotic DNA-dependent RNA polymerases.
Kwapisz M, Beckouët F, Thuriaux P.
Trends Genet. 2008 May;24(5):211-5.
Eukaryotic DNA-dependent RNA polymerases (Pol I-III) share a conserved core of 12 subunits, which is closely related to archaeal RNA polymerases. Rpb8, a subunit found in Pol I, II and III, was thought to be restricted to eukaryotes. We show here that Rpb8 closely resembles an archaeal protein called G, found only in Crenarchaea, which identifies a last missing link between the core structure of archaeal and eukaryotic RNA polymerases.
So the Rpb8 has likely been lost in various lineages of archaea meaning that the archaeal RNAP contains 7/8 yeast subunits that are not seen in the bacterial RNAP.
We are still left with the following question – Why in the world do archaea have such complex RNAPs ?