Eukaryotic RNA Polymerases

There are several different kinds of RNA that can be made when RNA polymerase copies a gene. The most common kind is messenger RNA (mRNA), which then goes on to be translated into protein by the translation machinery.

Another abundant RNA is ribosomal RNA (rRNA) of which there are three different versions in prokaryotes (23S, 16S, 5S) and four in eukaryotes (28S, 18S, 5.8S, 5S). Ribosomal RNA makes up the bulk of a ribosome and it is the catalyst of the reaction joining amino acid residues.

The third well-defined class of RNA is transfer RNA (tRNA). These are the molecules that carry amino acid residues into the active site of translation. They are responsible for the correct translation of mRNA sequence according to the genetic code.

The fourth class is a catch-all category called small RNAs. It includes a variety of RNA molecules that are involved in RNA processing, regulation, etc. Some of these RNAs are also catalytic RNAs.

All types of RNA are made by a single RNA polymerase in bacteria. The genes for each of the various types have distinct promoters but the bacterial RNA polymerase can bind to all of them with the help of specific transcriptional activators. This is not what happens in eukaryotes.

In eukaryotes there are five different RNA polymerases. RNA polymerase I has become specialized for transcription of the genes for the large ribosomal RNAs (class I genes). Eukaryotic cells need massive amounts of ribosomal RNA and they have many copies of ribosomal RNA genes arrayed head to tail. The electron micrograph below shows RNA polymerase I molecules in the act of transcribing adjacent ribosomal RNA genes (TU = transcription unit, NTS = non-transcribed spacer). Apparently, it was advantageous to select for a specialized RNA polymerase concentrating on producing ribosomal RNA.

RNA polymerase II is responsible for transcribing protein-encoding genes to produce mRNA (class II genes). It has evolved some special features that allow it to be coupled to the processing of mRNA precursors. Unlike bacteria mRNA, eukaryotic mRNA is modified at the 5′ and 3′ ends and the mNA precursor can be spliced.

The cartoon on the left illustrates another important difference between prokarotic and eukaryotic RNA polymerases (in this case RNAP II). The eukaryotic enzymes are all related to each other and to the bacterial enzymes. They share the same large subunits. But in addition to the homologous subunits the eukaryotic RNA polymerases have many more secondary subunits so they are quite a bit larger than their bacterial counterparts.

The eukaryotice enzymes also interact with a greater variety of transcription factors. In the example shown, the RNAP II core enzyme is associating with several transcription factors (TF) that are required for transcription initiation.

RNA polymerase III makes transfer RNA (tRNA), small ribosoma RNA (5S RNA) and most of the small RNAs that make up the fourth class of RNA (class II genes).

The 4th and 5th types of eukarytic RNA polymerases are the mitochondrial and chloroplast versions. As you might expect, these are similar to bacterial enzymes since they were transferred to eukaryotic cells during the endosymbiotic events that gave rise to mitochondrial and chloroplasts.

In the beginning it was confusing to sort out the various RNA polymerase activities in eukaryotic cells. The problem became much simpler when it was discovered that the mushroom toxin α-amanitin (left) (Mushrooms for Dinner) specifically inhibited RNA polymerase II and not RNA polymerase I. RNA polymerase III is somewhat inhibited in mammals but not in fungi or insects. This differential inhibition allowed workers to sort out the various RNA polymerases and their specificities.