8.8:
Eukaryotic RNA Polymerases
Eukaryotes have three different RNA Polymerases: RNA polymerase I, II, and III. They are structurally similar to one another and share common features with prokaryotic RNA polymerases, however, they transcribe different classes of RNA.
RNA Polymerase I transcribes most of the ribosomal RNA genes while RNA Polymerase III transcribes tRNA genes, some snRNA, and other small RNA genes.
The majority of protein-encoding RNA genes are transcribed by RNA polymerase II.
The carboxy-terminal domain of the RNA Polymerase II serves as a binding site for several transcription factors that regulate its enzymatic activity. The binding of these factors depends on the phosphorylation pattern of this domain.
8.8:
Eukaryotic RNA Polymerases
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the TATA-binding protein is common to all. These proteins remain attached to the RNAP to guide the direction of RNA synthesis on the template DNA strand. Once RNA strand elongation is complete, the RNAP and associated proteins need to disassemble and release the mRNA transcript.
Unlike the termination signals encoded by bacterial genes, the protein-encoding genes transcribed by RNA Polymerase II lack specific sequences that direct the enzyme to terminate at precise locations. The most common termination pathway, known as the Poly(A) dependent termination, combines polyadenylation of the mRNA transcript with RNAP termination. Here, while the RNA Polymerase II continues to transcribe RNA, sometimes up to thousands of basepairs past the end of the gene sequence, the transcript is cleaved at an internal site. Thus the upstream part of the transcript is released and a polyadenine tail can be added to the 3' end of the cleaved transcript. The downstream cleavage product is digested by a 5'-exonuclease while it is still being transcribed by the RNA Polymerase II. When the 5'-exonuclease digests all of the remainder transcripts, it helps the RNAP to dissociate from its DNA template strand, thus completing the transcription.
Suggested Reading
- Minakhin, Leonid, Sechal Bhagat, Adrian Brunning, Elizabeth A. Campbell, Seth A. Darst, Richard H. Ebright, and Konstantin Severinov. "Bacterial RNA polymerase subunit ω and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly." Proceedings of the National Academy of Sciences 98, no. 3 (2001): 892-897.
- Cooper GM. "The Cell: A Molecular Approach." 2nd edition. Sunderland (MA): Sinauer Associates; (2000). Eukaryotic RNA Polymerases and General Transcription Factors.
- Kuehner, Jason N., Erika L. Pearson, and Claire Moore. "Unravelling the means to an end: RNA polymerase II transcription termination." Nature reviews Molecular cell biology 12, no. 5 (2011): 283-294.