The enzyme RNA polymerase (RNAP) is present in all cells and is responsible for reading the genetic code stored in DNA. RNAP accomplishes this task by constructing RNA chains through a process termed transcription. In other words, RNAP is a nucleotidyltransferase that polymerises ribonucleotides in accordance with the information present in DNA. RNA polymerase enzymes are essential and are found in all organisms and many viruses.

Control of the process of transcription affects patterns of gene expression and thereby allows a cell to adapt to a changing environment, perform specialized roles within an organism, and maintain basic metabolic processes necessary for survival. Therefore, it is hardly surprising that the activity of RNAP is both complex and highly regulated. In E. coli bacteria, more than 100 factors have been identified which modify the activity of RNAP.

RNAP can initiate transcription at specific DNA sequences known as promoters. It then produces an RNA chain which is complementary to the DNA strand used as a template. The process of adding nucleotides to the RNA strand is known as elongation, and in eukaryotes RNAP can build chains as long as 2.4 million nucleosides (the full length of the dystrophin gene). RNAP will preferentially release its RNA transcript at specific DNA sequences encoded at the end of genes known as terminators.

Some RNA molecules produced by RNAP will serve as templates for the synthesis of proteins by the ribosome. Others can fold into enzymatically active ribozymes or tRNA molecules. A third option is that an RNA molecule will serve a purely regulatory role to control future gene expression (see siRNA).

RNAP accomplishes de novo synthesis. It is able to do this because specific interactions with the initiating nucleotide hold RNAP rigidly in place, facilitating chemical attack on the incoming nucleotide. Such specific interactions explain why RNAP prefers to start transcripts with ATP (followed by GTP, UTP, and then CTP). In contrast to DNA polymerase, RNAP includes a helicase activity, therefore no separate enzyme is needed to unwind DNA.

RNAP was discovered independently by Sam Weiss and Jerard Hurwitz in 1960. Ironically, by this time the 1959 Nobel Prize had been awarded to Severo Ochoa for the discovery of what was believed to be RNAP, but instead turned out to be a ribonuclease.

Classes of RNA Polymerases

In prokaryotic cells, all 3 RNA classes are synthesized by a single polymerase. In eukaryotic cells there are 3 distinct classes of RNA polymerase, RNA polymerase (pol) I, II and III. Each polymerase is responsible for the synthesis of a different class of RNA. The capacity of the various polymerases to synthesize different RNAs was shown with the toxin a-amanitin. At low concentrations of a-amanitin synthesis of mRNAs are affected but not rRNAs nor tRNAs. At high concentrations, both mRNAs and tRNAs are affected. These observations have allowed the identification of which polymerase synthesizes which class of RNAs. RNA pol I is responsible for rRNA synthesis (excluding the 5S rRNA).There are 4 major rRNAs in eukaryotic cells designated by there sedimentation size. The 28S, 5S 5.8S RNAs are associated with the large ribosomal subunit and the 18S rRNA is associated with the small ribosomal subunit. RNA pol II synthesizes the mRNAs and some of the small nuclear RNAs (snRNAs) involved in RNA splicing. RNA pol III synthesizes the tRNAs, the 5S rRNA and some snRNAs. back to the top

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