Like the RNA molecules in prokaryotic ribosomes, the eukaryotic rRNA molecules are also post-transcriptionally cleaved from larger transcripts. This processing, and the subsequent assembly of the large and small ribosomal subunits are carried out in the nucleolus, a region of the nucleus specialized for ribosome production, and containing not only high concentrations of rRNA and ribsomal proteins, but also RNA polymerase I and RNA polymerase III. In contrast, RNA polymerase II, as befits its broader purpose, is found throughout the nucleus.
Because of the density of material in the nucleolus needed for constant ribosome production, it is often readily visible under various types of microscopy despite not being bounded by a membrane.
The 40S small ribosomal subunit in eukaryotes also has just 1 rRNA, and has 33 proteins. The 60S, or large ribosomal subunit in eukaryotes has three rRNA molecules, two of which are roughly analogous to the prokaryote (28S and 5S eukaryotic, 23S and 5S prokaryotic), and one, the 5.8S, that binds with complementary sequence on part of the 28S rRNA. It also contains 50 proteins. These ribosomal subunits have roughly the same function as the prokaryotic versions: the small subunit in conjunction with various initiation factors is responsible for finding the start site and positioning the ribosome on the mRNA, while the large subunit houses the docking sites for incoming and spent aminoacyl-tRNAs and contains the catalytic component to attach amino acids via peptide bonds.
The ribosomal RNA precursors (pre-rRNA) are remarkably conserved in eukaryotes, with the 28S, 5.8S, and 18S rRNAs encoded within a single transcript. This transcript, synthesized by RNA polymerase I, always has the same 5’ to 3’ order: 18S, 5.8S, 28S. After the 45S pre-rRNA is transcribed, it is immediately bound by nucleolar proteins in preparation for cleavage and base modification. However, it is primarily the small nuclelolar RNAs (snoRNAs), not the proteins, that determine the position of the modifications. The primary modifications are 2’-hydroxylmethylation and transformation of some uridines into pseudouridines. These snoRNAs are sometimes transcribed independently by RNA polymerase III or II, but often are formed from the introns of pre-mRNA transcripts. Oddly, some of these introns come from pre-mRNAs that form unused mRNAs!
For the nucleolus to be the site of ribosome assembly, the ribosomal proteins must be available to interact with the rRNAs. By mechanisms discussed in the next chapter, the mRNAs for the ribosomal proteins are translated (as are all proteins) in the cytoplasm, but the resulting proteins are then imported into the nucleus for assembly into either the large or small ribosomal subunit. The subunits are then exported back out to the cytoplasm, where they can carry out their function.