Tuesday, March 20, 2007

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.


  1. How would one go about systemically naming a cyclopeptide anyhow? It sounds fantastically difficult...

  2. Don't forget RNA polymerase IV (Onodera et al., Cell 120, 613-622, 2005).

    Or the fact that chloroplasts possess two different RNA polymerases - the "bacterial" enzyme as well as a phage-type RNA polymerase. (The phage-type enzyme, I believe, is similar to the mitochondrial one. It is rather different from the bacterial enzyme.)

  3. I would love to know your thoughts on the "RNA world" theory. I have spent some time lately examining the spliceosome, snRNPs are neato!

  4. additionally, the arrow from DNA to RNA could be bidirectional instead of unidirectional when considering reverse transcriptase.
    cheers from st louis!

  5. "Apparently, it was advantageous to select for a specialized RNA polymerase concentrating on producing ribosomal RNA."

    ah-HA! Busted spinning an adaptationist just-so story! (I kid.)

  6. ...there are three different versions in prokaryotes and four in prokaryotes.

    Typo? Eukaryotes?

  7. an anonoymous person says,

    additionally, the arrow from DNA to RNA could be bidirectional instead of unidirectional when considering reverse transcriptase.

    Not to put too fine a spin on it but you raise an interesting point. I'm trying to convince people to use that diagram to represent the standard flow of information from DNA to protein and discourage them from claiming that it represents the Central Dogma of Molecular Biology.

    Thus, the arrows only go in one direction since that's the common way information flows.

    What you're suggesting is that the diagram should represent the theoretical concept called the sequence hypothesis. In that case, all known possiblities have to be included and this means adding another arrow to represent the extremely rare instances of reverse transcriptase [see Basic Concepts: The Central Dogma of Molecular Biology]. That's not what I want to do in this diagram.

  8. Why does our genome harbors multiple copies of Ribosomal RNA genes and only two copies each of Ribosomal Protein Coding genes? Considering the stoichiometry of Ribosomal RNA Vs Ribosomal protein required for Ribosome biosynthesis, why do our cells have an excess amount of ribosomal RNA?

    1. Protein-encoding genes are transcribed to produce a messenger RNA molecule (mRNA) and each mRNA can be translated into protein at least 10 or 20 times before it is degraded.

      The ribosomal RNA genes, on the other hand, are transcribed to produce functional ribosomal RNA that is immediately incorporated into ribosomes. Thus, in order to maintain the stoichiometry you need a lot more ribosomal RNA genes than ribosomal protein genes if transcription rate is limiting (which it is).