In the previous entry, I showed you how the eukaryotic cell plan is far more complex than the bacterial cell plan on multiple levels. We might add the existence of introns in protein-coding genes, and thus the need for a spliceosome, to the picture. And we’ll add more in the future. But for now, we have enough to acknowledge the existence of a mystery. Since bacteria teach us that life is possible without all this complexity, we can explore questions that remains in the collective blind spot of the non-teleologists – Why is the cell plan of the eukaryotic cell so needlessly complex?
We could try to explain this by invoking the large population sizes of bacteria and hypothesize that this difference is the consequence of purifying selection. After all, it is well known that natural selection streamlines bacteria for efficient replication. Yet while this may be part of the explanation, it leaves too many stones unturned. For example, does this mean that life originated from complex, rather than simple, beginnings, and natural selection has pruned away much of this ancient complexity? And how did the eukaryotic cell plan emerge in such a way as to escape the pruning shears of purifying selection? And why hasn’t purifying selection streamlined the machinery inside the yeast cell, an organism which exists as large populations?
To show you how deep this mystery goes, let’s focus on one example of needless complexity – the RNA polymerase.
As I mentioned before:
If we turn to transcription, bacteria employ a small set of transcription (sigma) factors and use an RNA polymerase (RNAP) built from four subunits. Among eukaryotes, we find 100s of different transcription factors and the single RNAP has been expanded into three versions: RNAP I, RNAP II,and RNAP III. RNAP II is most similar to the bacterial version, yet if we focus just on this protein complex, we again find enhanced complexity, where the eukaryotic version contains up to 15 subunits.
In bacteria, the RNAP is built from four different subunits, but in eukaryotes, it is built from up to 15 subunits. Yet both versions of the protein machine carry out the same essential function – linking the DNA world to the amazing world of proteins through the process of transcription (synthesizing an RNA molecule from a DNA template). But what if we also surveyed the third domain, the Archaea? Archeabacteria were long thought to be little more than exotic bacteria, given they are the same size
and possess the same level of cytoplasmic complexity as eubacteria.
Surely the streamlining hypothesis would predict that the archaeal RNAP would be similarly complex as the eubacterial RNAP.
But that is not what we see. Here is a figure that documents the RNAP subunits from the three domains, where homologs are identified by using the same color:
Goodness me. The archaeal RNAP is not only much more complex than the bacterial version, but it is very similar to the complex eukaryotic RNAP. Like I said, while streamlining may be part of the explanation, it leaves too many stones unturned. Why in the world do Archaea have such complex RNAPs? Eubacteria teach us that such complexity is not needed for the bacterial way of life. Yet there it is, as one of the defining features of the archaeal domain.
In the next entry, we’ll take up this question.