Usually, all eukaryotes have three different types of RNA polymerases (RNAPs) which transcribe different types of genes. RNA polymerase I transcribes rRNA genes, RNA polymerase II transcribes mRNA, miRNA, snRNA, and snoRNA genes, and RNA polymerase III transcribes tRNA and 5S rRNA genes.
Bacteria and archaea only have one RNA polymerase. But eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a clear subset of RNA:
RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol.
RNA polymerase IV and V found in plants are less understood; they make siRNA. In addition to the ssRNAPs, chloroplasts also encode and use a bacteria-like RNAP.
RNA polymerase I
RNA polymerase I synthesizes a pre-rRNA 45S (35S in yeast), which matures and will form the major RNA sections of the ribosome.
This enzyme is located in the nucleolus of the cell. The rRNA is component elements of the ribosomes and is important in the process of translation. Therefore, RNA polymerase I synthesize almost all rRNAs except 5S rRNA. In yeast, the enzyme has a mass of 600kDa and 13 subunits.
RNA polymerase II
RNA polymerase II synthesizes precursors of mRNAs and most sRNA and microRNAs. This enzyme is present in the nucleus. Most organisms that have RNA polymerase II have a 12-subunit RNAP II (with a mass of about 550 kDa). It is structurally made up of holoenzyme and mediators, with General Transcriptional factors (GTFs). They have transcription factors and transcriptional regulators. It functions by synthesizing all proteins that code for the nuclear pre-mRNAs in eukaryotic cells (mRNAs in prokaryotic cells). It is responsible for transcribing most of the eukaryotic genes and especially found in human genes.
RNA polymerase III
It is present in the nucleus. The RNA polymerase III has 14 or more distinct subunits with a mass of approximately 700 kDa. Its function is to transcribe transfer RNA (tRNA), ribosomal RNA (rRNA), and other small RNAs. Some of its target points are important for the normal functioning of the cell
RNA polymerases IV and V
They are exclusively found in plants, and they perform combined action in the formation of small interfering RNA and heterochromatin in the cell nucleus. In Plants, the RNA polymerase is found in the chloroplast (plastids) and mitochondria, encoded by the mitochondrial DNA. These enzymes are much more related to bacterial RNA polymerase than to the nuclear RNA polymerase. Their function is to catalyze specific transcription of organelle genes.
Features of RNA polymerase
The prokaryotes have a single type of RNA polymerase (RNAP) which synthesizes all the classes of RNA, i.e mRNA, tRNA, rRNA, sRNA.
The RNA Polymerase molecule is made up of 2 domains and 5 subunits:
- Core and holoenzyme
- Subunits (β, β’, α (αI and αII), ω,)
- The ‘a’ subunit is made up of two distinct domains. The N-terminal domain (a-NTD) and the C-terminal.
The N-terminal is involved in dimerization forming a2 and further assembly of the RNA polymerase. The C-terminal domain functions such as binding to the Upstream Promoter (UP) DNA sequence at promoters for rRNA and tRNA genes and in communication with several transcriptional activators.