As we are about to explore possible mechanisms by which the Rpb4 protein could nudge the evolutionary emergence of eukarya and/or metazoa, I want to set the stage by briefly reviewing two fundamental themes.
First, one of the primary ways in which eukaryotic cells differ from prokaryotic cells revolves around the nucleus.
The membrane-bound nucleus represents a very significant example of one of the pillars of PICERAS – compartmentalization. This figure should help you visualize why the nucleus is so significant:
The nuclear membrane makes it possible to sequester the DNA from the ribosomes. This means the process of transcription (RNA synthesis) is decoupled from the process of translation (protein synthesis). The decoupling opens up a huge regulatory window, as RNA can be massively processed before it is sent out of the nucleus to be translated. One example of such processing is alternative splicing, something that probably facilitated the emergence of complex metazoan life. We’ve seen that bacteria lack protein-coding introns and this is not surprising given that bacteria usually couple the process of transcription and translation, such that the begins translating the mRNA before the RNA polymerase is finished making the mRNA:
Second, in The Design Matrix, I lay out the logic of multifunctional, moonlighting proteins as mechanisms to front-load evolution. Recently, I successfully employed this logic to predict that most ribosomal proteins would have functions apart from their role in the ribosome. You can read about this here (check out section 4).
Got it? The emergence of the nucleus poses a radical change, as a process built around the coupling of transcription and translation must now be decoupled. And the front-loading hypothesis has already been successful when it comes to predicting moonlighting proteins. Let’s tie these together in the context of our needlessly complex archaeal RNA polymerase.