MoBio RNA Polymerases Chapter 4

The function of RNA polymerases

Both RNA and DNA polymerases can add nucleotides to an existing strand, extending its length. However, there is a major difference between the two classes of enzymes: RNA polymerases can initiate a new strand but DNA polymerases cannot. Therefore, during DNA replication, an oligonucleotide (called primer) should first be synthesized by a different enzyme.

The chemical reaction catalyzed by RNA polymerases is shown in Figure 4-B-2. The nucleotides used to extend a growing RNA chain are ribonucleoside triphosphates (NTPs). Two phosphate groups are released as pyrophosphate (PPi) during the reaction. Strand growth is always in the 5' to 3' direction. The first nucleotide at the 5' end retains its triphosphate group (Figure 4-B-3).

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Figure 4-B-2. The chemical reaction catalyzed by RNA polymerases.

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Figure 4-B-3. Simplified presentation for the chain elongation. The vertical line represents the pentose and the slanting line denotes the phosphodiester bond. Bases are designated as N1, N2, etc.

Classes of RNA polymerases

E. coli

An E. coli RNA polymerase is composed of five subunits: two α subunits, and one for each β, β', and σ subunit. β (151 kD) and β' (156 kD) are significantly larger than α (37 kD). Several different forms of σ subunits have been identified, with molecular weights ranging from 28 kD to 70 kD. The σ subunit is also known as the σ factor. It plays an important role in recognizing the transcriptional initiation site, and also possesses the helicase activity to unwind the DNA double helix. Nucleotide synthesis is carried out by other four subunits, which together are called the core polymerase. The term holoenzyme refers to a complete and fully functional enzyme. In this case, the holoenzyme includes the core polymerase and the σ factor.

Eukaryotes

There are three classes of eukaryotic RNA polymerases: I, II and III, each comprising two large subunits and 12-15 smaller subunits. The two large subunits are homologous to the E. coli β and β' subunits. Two smaller subunits are similar to the E. coli α subunit. However, the eukaryotic RNA polymerase does not contain any subunit similar to the E. coli σ factor. Therefore, in eukaryotes, transcriptional initiation should be mediated by other proteins.

RNA polymerase II is involved in the transcription of all protein genes and most snRNA genes. It is undoubtedly the most important among the three classes of RNA polymerases. The other two classes transcribe only RNA genes. RNA polymerase I is located in the nucleolus, transcribing rRNA genes except 5S rRNA. RNA polymerase III is located outside the nucleolus, transcribing 5S rRNA, tRNA, U6 snRNA and some small RNA genes.