What is RNA polymerase?
RNA polymerase is the name given to a class of enzyme which in vivo synthesize RNA molecules using double stranded DNA as a template. Such enzymes are more properly known as DNA – depending RNA polymerases.
The copying of the information contained in a DNA sequence into an RNA sequence is termed ‘transcription,’ a central step in biological information flow. RNA polymerase is the key enzyme involved in transcription.
Some RNA viruses encode enzymes which synthesize RNA from an RNA template. Typically, such an enzyme is called an ‘RNA replicase,’ but occasionally the term ‘RNA dependent RNA polymerase’ is used. These enzymes are distinct from the RNA polymerase we are discussed here.
All RNA polymerase synthesizes an RNA chain from the 5’ end to the 3’ end, the template strand of the DNA is consequently read in the antiparallel 3’ to 5’ direction, since templating requires base pairing.
The substrate is ATP, GTP, CTP, UTP and also magnesium ion is required. The RNA molecules are synthesized from specific starting sites on the DNA (called promoter), and RNA polymerase can initiate new chain without the requirement for a primer, unlike the case with DNA polymerase have essentially identical mechanism of phosphodiester bond formation during elongation.
Cellular RNA polymerase are multi subunit enzymes. Bacteria and Archaea each have a single RNA polymerase, while the eukaryotic nucleus contains three such enzymes: RNA polymerase I (RNAP I), RNA polymerase II (RNAP II), and RNA polymerase III (RNAP III) two non-redundant plant-specific RNA polymerases, Pol IV and Pol V, have been identified and shown to generate noncoding RNAs that are required for transcriptional gene silencing via the RNA-directed DNA methylation (RdDM) pathway.
While there are profound differences between these multi subunit RNA polymerases, there are also significant similarities. Indeed, it is clear that these enzymes are all related and form a family. All members of this family have three different subunits, which are evolutionarily conserved to a greater or lesser extent.
Bacterial RNA polymerase and the closely related chloroplast RNA polymerase contain only these conserved subunits. The Archaea, like the Bacteria, have only a single RNA polymerase, but it is more complex than a bacterial enzyme and is more complex eukaryotic RNA polymerase II.
However, even in the complex eukaryotic RNA polymerases, conserved sequences make up over 50% of the enzyme mass, and therefore the simpler bacterial enzyme has provided an important model for RNA polymerase structure and function. This has been confirmed by structural analysis of the purified enzymes.
However, not all RNA polymerase are multi subunit enzymes. The enzymes found in mitochondria (but encoded in the nucleus) and those encoded by some bacteriophages are single subunit enzymes. These single subunit enzymes are not closely related to the complex cellular RNA polymerases but are more closely related to certain DNA polymerases.
Types of RNA polymerase (DNA dependent RNA polymerase)
As we discuss above Bacteria, Viruses and Archaea have a single type of RNA polymerase that synthesizes all the subtypes of RNA, while multicellular organisms have 5 different types of RNA polymerases which perform different functions in the synthesis of different RNA molecules.
Bacterial RNA polymerase (Prokaryotic RNA polymerase)
Bacteria have a single cellular RNA polymerase (RNAP), whose ‘holoenzyme’ form have five subunits
- Two copies of relatively small α-subunit (each about 36 kDa),
- One copy each of large β and β′- subunits (151 kDa and 155 kDa, respectively)
- One copy of the σ- subunit, also called the ‘sigma factor.’
The core enzyme, of about 400 kDa, contains all the subunit except σ and can carry out the elongation reaction of polymerization using a DNA template and the four substrates ATP, CTP, GTP and UTP.
The evolutionary conserved subunits are those that make up the core. However, site-specific initiation requires the σ subunit, which allows RNAP to recognize the promoter. Most bacteria encode several alternative σ factors (E. Coli encode 7, Bacillus subtilis encodes 17), which may very widely in size and which allow the RNAP to recognize several different types of promoters.
If there are several different factors in cell, there must be several different holoenzymes and, therefore one could say there are several RNA polymerases in a given bacterium.
However, this would be misleading, because the σ factor (of whatever kind) is only bound t the enzyme during initiation.
Also, in a given bacterium, the majority of genes typically require only a single species of sigma factor and, therefor one form of the holoenzyme predominates. In E. coli the primary σ factor, and the first discovered, has a mass of 70 kDa and is often referred to as σ70 .
Initiation of transcription by RNAP at the promoter is a complex process involving many different steps. First, of course, the core enzyme must bind the appropriate σ factor. The holoenzyme then binds to promoter DNA upstream of the transcriptional start site.
RNAP then interacts with the DNA, leading to melting of about 14 bp of the promoter DNA, including the transcriptional start site. There is also a conformational change of the RNAP during this process.
RNAP can then begin RNA synthesis, but chain elongation often aborts, yielding short chai of less than 10 nucleotides. However, RNAP remains at the promoter and can undergo further rounds of abortive synthesis or true elongation. If the chain reaches about 10 nucleotides in length, σ factor is released and the core RNAP begins moving along the DNA template, synthesizing the RNA chain.
The newly synthesized chain exits the RNAP through a channel. The rate of elongation of an RNA chain in vivo may be about 50 nucleotides per second, but this rate is the mean of rapid elongation over some sequences and pauses at other. The elongating complex is quite stable, but the RNAP also terminates at specific DNA sequences, termed ‘transcription terminators.’ Some such sequences can be recognized by the RNAP itself, but others require specific accessory proteins, called ‘termination factors.’
Eukaryotic RNA polymerases
RNAP I, RNAP II, and RNAP III of the eukaryotic nucleus are quite different from each other structurally and each transcribes a different set of genes (other polymerases are located in the mitochondria and chloroplasts).
However, all three have two large subunits that are related to each other and also to the two largest subunit o the bacterial RNAP. In addition, several of the smaller subunits are found in commo among all three of these enzymes, or only between RNAP I and RNAP III.
As with the bacterial RNAPs, there are special accessory factor needed for transcription initiation. However, unlike the case in bacteria, the eukaryotic initiation factors recognize the promoter elements independently, not as part of a polymerase holoenzyme.
Many different initiation factors are involved, particularly in genes transcribed by RNAP II, and some of the initiation factor are themselves very complex proteins. Purified eukaryotic RNA polymerases, then, cannot selectively initiate transcription at promoters.
The term holoenzyme is sometime used to refer to a eukaryotic RNAP, but in this case it refers to something more like the bacterial ‘core’ enzyme and would not be able to initiate from promoters. However, unlike the bacterial core enzyme eukaryotic holoenzyme may contain a large number of other proteins involved in transcription or the processing of RNA.
1) RNA polymerase I
- RNA polymerase I is found in the nucleolus and transcribes only gene encoding large ribosomal RNAs, the majority of the cellular RNA synthesized.
- In Yeast the enzyme has 13 subunits (and a mass of almost 600 kDa).
- Five of the smaller subunits are also found in yeast RNAP II and III and two others in RNAP III.
2) RNA polymerase II
- RNA polymerase II transcribes genes which encode proteins, the majority of genes in a cell. It also transcribes genes encoding most of the small nuclear RNAs (snRNAs).
- Most organisms seem to have a 12- subunit RNAP II (with a mass of about 550 kDa). However, several other proteins are required for complete activity and the RNAP holoenzyme may have a mass of 4000 kDa.
3) RNA polymerase III
- RNA polymerase III primarily transcribes genes encoding transfer RNA and 5S RNA but also transcribes some genes encoding other small RNAs.
- RNAP III has 14 or more distinct subunit with a mass of almost 700 kDa,
- Although the promoters for RNA polymerase I and RNA polymerase II lie for the most part upstream of the transcription start site (as is the case for prokaryotic promoters), some promoters for RNA polymerase III lie downstream of the start site.
4) RNA polymerase IV and V
- They are two non-redundant plant-specific RNA polymerases, RNAP IV and RNAP V, have been identified and shown to generate noncoding RNAs that are required for transcriptional gene silencing via the RNA-directed DNA methylation (RdDM) pathway.
- In plant, the RNA polymerase is found in the chloroplast and mitochondria, encoded by mitochondrial DNA.
- These enzymes are much more related to bacterial RNA polymerase then to the nuclear RNA polymerase.
The overall elongation complexes formed by these enzymes seem similar to those of the bacterial RNAPs although the mechanism by which these enzymes locate promoters are quite different from that used by bacteria, the overall mechanism of transcriptional initiation, including abortive cycles, is very similar.
All eukaryotes have three different RNA polymerases (RNAPs) which transcribe different types of genes. RNA polymerase I transcribes rRNA genes, RNA polymerase II transcribes mRNA, miRNA, snRNA, and snoRNA genes, and RNA polymerase III transcribes tRNA and 5S rRNA genes.