Eukaryotes: Needlessly Complex

It is well known that eukaryotic cells are more complex than prokaryotic cells. For example, while the typical eukaryotic cell is 10-100 micrometers in diameter, contains numerous membranous organelles, has an elaborate cytoskeleton, and reproduces through mitosis, the typical bacterial cell is only 0.2-2.0 micrometers in diameter, lacking organelles and cytoskeleton (or so it was thought), while reproducing through binary fission. Clearly, the cytological complexity of the eukaryotic cell is not needed in order to be alive.

Yet the theme of needless complexity repeats itself at increasingly smaller scales like a fractal image.

Consider, for example, the three basic universal processes of information transfer: DNA replication, transcription, and translation. In both bacteria and eukaryotes, the same building blocks are used, the same macromolecules are synthesized, and the processes are essentially the same. Yet in each case, the process is more complex among eukarya than in bacteria. For example, while bacteria replicate their single chromosome from a single origin point and possess five different DNA polymerases, eukaryotes initiate replication from multiple points on their multiple chromosomes (involving a process known as licensure and contain at least 19 DNA polymerases.

If we turn to transcription, bacteria employ a small set of transcription (sigma) factors and use an RNA polymerase (RNAP) built from five 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. And when we compare the shared core subunits, the eukaryotic versions even have additional domains (Cramer, Patrick. 2002 Multisubunit RNA polymerases. Current Opinion in Structural Biology 12:89-97).

And then there is the classic example of the bacterial and eukaryotic ribosomes. As can be seen from the table below, the eukaryotic ribosome has many more proteins (for both subunits) and longer ribosomal RNAs in each subunit.

Comparison of Ribosome Structure in Bacteria and Eukaryotes
Bacterial (70S) Eukaryotic (80S)
Large Subunit 50S 60S
(1 of each)
23S (2904 nts) 28S (4700 nts)
5S (120 nts) 5S (120 nts)
5.8S (160 nts)
Proteins 33 ~49
Small Subunit 30S 40S
rRNA 16S (1542 nts) 18S (1900 nts)
Proteins 20 ~33

[Source for table]

Finally, if we consider the entire proteome from Eukarya, Bacteria, and Archaea, the theme of needless complexity is ubiquitous (Brocchieri, L and Karlin, S. Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Research 33: 3390–3400). The median length of the proteins annotated among Eukaryotes is 361 amino acids while it is only 267 amino acids in Bacteria and 247 amino acids in Archaea. This is a theme that is seen among all the various functional classes of proteins, as seen from some examples in the table below.

Median Length of Proteins (amino acids)
Bacterial Eukaryotic
DNA replication and processing proteins 315 723
Transcription-related proteins 240 444
Translation-related proteins 208 296
Cell division and chromosome partitioning 346 439
Inorganic ion transport and metabolism 314 538
Signal transduction mechanisms 323 605

(modified from Brocchieri and Karlin)

The theme of needless complexity among eukarya is seen from many different perspectives: the global architecture of the cell, the number of steps involved in many basic processes, the number of components in any machine, and the size of proteins regardless of function. Needless complexity thus permeates the eukaryotic cell.

And this leaves us with some tantalizing questions. Why is the eukaryotic cell plan so much more complex than the bacterial cell plan? What does this increased complexity tell us about the eukaryotic cell plan relative to the bacterial version? Why does the theme of needless complexity reach into every aspect of the cell plan?

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