The front-loading hypothesis, under the guidance of PREPA, allows us to formulate a testable hypothesis – the “bells and whistles” of the archaeal RNAP – Rpb 4, 5, 7, 10, 11, and 12 – will play crucial roles in the emergence of a) the eukaryotic cell and/or b) complex, metazoan life.
To test this hypothesis, let’s go back to that assembly map. The first thing that stood out to me was Rbp4 and 7 (which is E and F in archaea). These two look like they interact with the core machine as a dimer (a combination of both proteins) and in cell biology, dimerization is a useful regulatory node. In other words, the bells and whistles of the archaeal RNAP might represent preadaptations that would nudge the ability to regulate the RNAP in ways that would assist the emerging complexity entailed in the appearance of eukarya, then metazoa. So the telic perspective would allow us to predict these two proteins play some form of regulatory role. With this hypothesis in hand, it was once again time to probe the literature. Over the next few days, let me share some of the things I found.
First, let’s begin with E and F in archaea. It turns out the PREPA pattern begins to take hold, as subunit F, and probably E, are not required for archaebacteria to survive:
The results reported demonstrate that the F subunit of RNAP is not essential for T. kodakarensis viability and as RNAP isolated from the T. kodakarensis DrpoF mutant also lacks subunit E, it seems possible that subunit E is also not essential for archaeal transcription in vivo. Consistent with this, the core enzyme purified from T. kodakarensis KUWLFB, which lacks both subunits E and F, was fully active in transcription initiation, elongation and termination in vitro. 
Yet E and F are not useless, as these RNAP parts are needed for the archaebacteria to grow efficiently at high temperatures. Apparently, E and F are used to activate genes needed to thrive at such temperatures, meaning they do have some form of regulatory role.
When we turn to baker’s yeast, we see the same theme:
The relative levels of Rpb4 and Rpb7 in yeasts affect the differential gene expression and stress response. Rpb4 is nonessential in S. cerevisiae and affects expression of a small number of genes under normal growth conditions. 
So Rpb4 (F in archaea) is not need to live, but instead is used to facilitate existence under stressful environmental conditions. Sounds like a regulatory node that will one day come in very handy when it is time to unfold a eukaryotic cell or metazoan body plan. In fact, now consider this:
The pol II enzyme consists of 12 subunits, which are highly conserved during evolution. The specific functions of the smaller subunits such as Rpb4 are relatively poorly understood, and they can show differences between organisms. For example, Rpb4 is essential in mammals and fission yeast (Schizosaccharomyces pombe), but not in budding yeast (Saccharomyces cerevisiae). Here we use fission yeast as a model to learn more about particular roles of Rpb4 in genome-wide transcription. 
Did you see that? Rpb4 is not essential in archaea or single-celled baker’s yeast, but is essential in multicellular fungi and animals. It looks like one of the gadgets on the needlessly complex archaeal RNAP has been recruited to play a key role in the existence of multicellularity. Can you say pre adap ta tion?
So let’s pause here and let you take this in. Next, let’s look more closely at what Rpb4 is doing.