RNA polymerase

RNA polymerase (RNAP) is the enzyme which does transcription.The 2006 Nobel Prize in Chemistry was awarded to Roger D. Kornberg for creating detailed molecular images of RNA polymerase during various stages of the transcription process.

RNA polymerase (RNAP) in action. It is building a messenger RNA molecule from a DNA helix. Part of the enzyme was made transparent so the RNA and DNA can be seen. The magnesium ion (yellow) is located at the enzyme active site

With the help of some other molecules, it makes messenger RNA from a strand of a DNA. This is its main function, but it does various other things. Products of RNAP include:

• Messenger RNA (mRNA). These are templates for the synthesis of proteins by ribosomes.
• Non-coding RNA or "RNA genes". These are a broad class of genes that encode RNA which is not translated into protein. The most important RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought.
  • Transfer RNA (tRNA)—transfers specific amino acids to growing polypeptide chains at the ribosomal site of protein synthesis during translation
  • Ribosomal RNA (rRNA)—a component of ribosomes
  • Micro RNA—regulates gene activity
  • Catalytic RNA (Ribozyme)—enzymatically active RNA molecules

In eukaryotes

Structure of eukaryotic RNA polymerase II (light blue) in complex with α-amanitin (red), a strong poison found in death cap mushrooms that targets this vital enzyme

Eukaryotes have various RNAPs in their nuclei, each to synthesis a type of RNA. All are similar and related to each other and to bacterial RNAP:

• RNA polymerase I synthesizes a pre-rRNA which will form the major RNA sections of the ribosome.
• RNA polymerase II synthesizes precursors of mRNAs and most snRNA and microRNAs. This is the most studied type. It needs a range of transcription factors to bind it to promoters.
• RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol.
• RNA polymerase IV synthesizes siRNA in plants.
• RNA polymerase V synthesizes RNAs involved in siRNA-directed heterochromatin formation in plants.

Eukaryotic chloroplasts have an RNAP very similar to bacterial RNAP ("plastid-encoded polymerase"). Eukaryotic chloroplasts also have a second, unrelated, RNAP.

Eukaryotic mitochondria contain an unrelated RNAP (member of the "single-subunit RNAP" protein family).

X-ray crystallography of DNA and RNA polymerases show that, other than having a Mg²⁺ ion at the catalytic site, they are virtually unrelated to each other. So the two classes of enzyme have arisen independently twice in the early evolution of cells. One line led to the modern DNA polymerases and reverse transcriptases. The other line led to all modern cellular RNA polymerases.