RNA
Polymerases
Synthesis - RNA synthesis involves the copying of a template DNA strand by RNA polymerase. Though several different types of RNA polymerase are known, all catalyze the following basic reaction,
using the rules of complementarity (A-T, G-C, C-G, and U-A, where the bases of ribonucleosides are listed first in each pair and the bases of deoxyribonucleosides are listed second).
Prokaryotic RNA polymerase - A single RNA polymerase catalyzes the synthesis of all three E. coli RNA classes--mRNA, rRNA, and tRNA. This was shown in experiments with rifampicin (Figure 26.4a), an antibiotic that inhibits RNA polymerase in vitro and blocks the synthesis of mRNA, rRNA, and tRNA in vivo.
Eukaryotic RNA polymerases - Eukaryotes contain three distinct RNA polymerases,
one each for the synthesis of the three larger rRNAs, mRNA, and
small RNAs (tRNA plus the 5S species of rRNA). These are
called RNA polymerases I (see here),
II (here), and
III (here), respectively.
The enzymes differ in their sensitivity to inhibition by 
-amanitin (Figure
26.4b), a toxin from the poisonous Amanita mushroom.
RNA polymerase II is inhibited
at low concentrations, RNA polymerase
III is inhibited at high concentrations, and RNA
polymerase I is quite resistant.
Other transcriptional inhibitors - Cordycepin (3'-deoxyadenosine) (Figure 26.4c), is a transcription chain terminator because it lacks a 3' hydroxyl group from which to extend. The nucleotide of cordycepin is incorporated into growing chains, confirming that transcriptional chain growth occurs in a 5' to 3' direction. Another important transcriptional inhibitor is actinomycin D (Figure 26.4d), which acts by binding to DNA. The tricyclic ring system (phenoxazone) intercalates between adjacent G-C base pairs, and the cyclic polypeptide arms fill the nearby narrow groove.
DNA polymerase vs. RNA polymerase - Vmax (see here) for the DNA polymerase III holoenzyme, at about 500 to 1000 nucleotides per second, is much higher than the chain growth rate for bacterial transcription-50 nucleotides per second, which is the same as Vmax for purified RNA polymerase. Although there are only about 10 molecules of DNA polymerase III per E. coli cell, there are some 3000 molecules of RNA polymerase, of which half might be involved in transcription at any one time.
Replicative DNA chain growth is rapid but occurs at few sites, whereas transcription is much slower, but occurs at many sites. The result is that far more RNA accumulates in the cell than DNA. Like the DNA polymerase III holoenzyme, the action of RNA polymerase is highly processive. Once transcription of a gene has been initiated, RNA polymerase rarely, if ever, dissociates from the template until the specific signal to terminate has been reached.
Accuracy of template copying - Another important difference between DNA and RNA polymerases is the accuracy with which a template is copied. With an error rate of about 10-5, RNA polymerase is far less accurate than replicative DNA polymerase holoenzymes, although RNA polymerase is much more accurate than would be predicted from Watson-Crick base pairing (see here) alone. Recent observations suggest the existence of error-correction mechanisms. In E. coli, two proteins, called GreA and GreB, catalyze the hydrolytic cleavage of nucleotides at the 3' ends of nascent RNA molecules. These processes may be akin to 3' exonucleolytic proofreading by DNA polymerases. The following, however, are important differences:
1. Cleavage of 3' ends of RNA molecules usually removes oligonucleotides, rather than single nucleotides, and
2. The rate of hydrolysis is much lower than the rate of RNA chain extension by RNA polymerase.
The mechanism of transcriptional error correction is still an open question and the subject of ongoing research efforts.
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