Eukaryotic transcription is a complex mechanism that requires the interactions of a variety of components. Therefore, in describing the mechanism, it is important to first provide a framework for the components involved. A discussion on how these components work together to produce mRNA will then follow.
In eukaryotes, there are three DNA-dependent nuclear RNA polymerases that transcribe DNA into the following products: RNA polymerase I produces ribosomal RNA (rRNA), RNA polymerase II produces messenger RNA (mRNA), and RNA polymerase III produces transfer RNA (tRNA) and 5s ribosomal RNA (1). Each of these enzymes is comprised of 8-14 subunits and interacts with additional factors used for promoter recognition and activating initiation.
RNA Polymerase II Structure:
Eukaryotic RNA Polymerase II contains 12 subunits, Rpb1 to Rpb2 . These subunits can be placed into three main groups: the core subunits, the common subunits, and the non-essential subunits. The Jmol image on the left shows ten of these subunits in colors corresponding to the diagram above.
The core subunits Rpb1, Rpb2, and Rpb3, resemble those of prokaryotic RNA polymerase (alpha, beta prime, and beta). The functions of Rpb1 and Rpb2 mimic the beta and beta primeβ subunits respectively. Whereas Rpb3 along with Rpb11 combine to form a heterodimer that resembles the alpha subunit, but to a lesser degree. Rpb1’s role is to bind DNA and help select where on the DNA transcription will begin (start site selection). Similarly, Rpb2 contains the active site to which DNA binds and mRNA is produced. This subunit also helps with start site selection. In fact, during DNA binding, the DNA fits perfectly into a cleft or groove formed by both Rpb1 and Rpb2. Lastly, Rpb3 along with Rpb11 is thought to form a heterodimer as stated above. During the formation of a complex necessary to initiate transcription (pre-initiator complex), this heterodimer may bind to another site on the promoter region (UP-element site). This serves to anchor the enzyme to the promoter and ensure tighter binding of the complex.
The largest of these three, Rpb1, also contains a carboxy terminus domain (CTD), which is a sequence of amino acids at one end of the protein. This domain consists of a conserved sequence that is repeated several times. The function of the CTD depends on whether or not the domain contains a phosphate group. During transcription initiation, the Rpb1 subunit is its dephosphorylated state (IIA). This state allows RNA polymerase II to form a complex necessary to initiate transcription (pre-initiator complex). However, during elongation, the Rpb1 subunit is its phosphorylated state (IIo). This allows the enzyme to complex with different factors and promote the elongation stage of transcription. Conversion between these two states is important for the switch between the initiation and elongation steps of transcription.
Rpb5, Rpb6, Rpb8, Rpb10, and Rpb12 are grouped into the common subunit category, because they are found in RNA polymerase I, II, and III. Less is known about these subunits, but they are necessary transcription.
Very little is known about the nonessential subunits Rpb4, Rpb7, Rpb9, and Rpb11. It was thought that these subunits were not required for transcription. However, some studies on yeast have shown that Rpb4 and Rpb7 form a sub-complex when RNA polymerase II is place under different environmental conditions. This sub-complex may bind DNA and initiate transcription in response to these new conditions.
