What is RNA polymerase?
RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence, duyring the process of transcription.
As complex molecule composed of protein subunits, RNA polymerase controls the process of transcription, during which the information stored in a molecule of DNA is copied into a new molecule of messenger RNA.
RNA polymerases have been found in all species, but the number and composition of these proteins vary across taxa. For instance, bacteria contain a single type of RNA polymerase, while eukaryotes (multicellular organisms and yeasts) contain three distinct types.
In spite of these differences, there are striking similarities among transcriptional mechanisms. For example, all species require a mechanism by which transcription can be regulated in order to achieve spatial and temporal changes in gene expression.
RNA polymerase structure and function (in transcription)
The RNA polymerase enzyme is a large complex made up of multiple subunits1. The prokaryotic form of RNA polymerase has four subunits capable of transcribing all types of RNA. In eukaryotes, these enzymes have eight or more subunits that facilitate the attachment and processing of DNA throughout transcription.
The three stages of transcription involve various functions of RNA polymerase that result in the synthesis of RNA:
1. Initiation
Initiation begins when RNA polymerase wraps around the promoter region of DNA. The promoter is a DNA sequence that guides RNA polymerase on where to bind upstream of a gene.
While prokaryotic RNA polymerase can directly bind to DNA promoter sequences, eukaryotic forms require the assistance of transcription factors for initial binding.
Once RNA polymerase successfully binds DNA at the targeted promoter region, the enzyme can continue with the second stage of transcription.
2. Elongation
Elongation commences when RNA polymerase unwinds double-stranded DNA into two single strands. These DNA strands are used as genetic templates for RNA synthesis.
As the DNA template strand moves through the RNA polymerase it builds an RNA strand that is complimentary to the transcribed DNA strand.
3. Termination
Termination is the final step of transcription. Once RNA polymerase encounters a terminator sequence or signal, it stops adding complementary nucleotides to the RNA strand.
This is followed by the release of the RNA transcript, which marks the end of transcription for that template of DNA.
Types Of RNA Polymerase
In prokaryotes
In bacteria, the same enzyme catalyzes the synthesis of mRNA and non-coding RNA (ncRNA).
RNAP is a large molecule. The core enzyme has five subunits (~400 kDa):
β′ RNA Polymerages
The β′ subunit is the largest subunit, and is encoded by the rpoC gene. The β′ subunit contains part of the active center responsible for RNA synthesis and contains some of the determinants for non-sequence-specific interactions with DNA and nascent RNA. It is split into two subunits in Cyanobacteria and chloroplasts.
β RNA Polymerages
The β subunit is the second-largest subunit, and is encoded by the rpoB gene. The β subunit contains the rest of the active center responsible for RNA synthesis and contains the rest of the determinants for non-sequence-specific interactions with DNA and nascent RNA.
α (αI and αII) RNA Polymerages
Two copies of the α subunit, being the third-largest subunit, are present in a molecule of RNAP: αI and αII (one and two). Each α subunit contains two domains: αNTD (N-terminal domain) and αCTD (C-terminal domain).
αNTD contains determinants for assembly of RNAP. αCTD (C-terminal domain) contains determinants for interaction with promoter DNA, making non-sequence-non-specific interactions at most promoters and sequence-specific interactions at upstream-element-containing promoters, and contains determinants for interactions with regulatory factors.
ω RNA Polymerages
The ω subunit is the smallest subunit. The ω subunit facilitates assembly of RNAP and stabilizes assembled RNAP.
In order to bind promoters, RNAP core associates with the transcription initiation factor sigma (σ) to form RNA polymerase holoenzyme.
Sigma reduces the affinity of RNAP for nonspecific DNA while increasing specificity for promoters, allowing transcription to initiate at correct sites. The complete holoenzyme therefore has 6 subunits: β′βαI and αIIωσ (~450 kDa).
In Eukaryotes
Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA. All are structurally and mechanistically related to each other and to bacterial RNAP:
- RNA polymerase I synthesizes a pre-rRNA 45S (35S in yeast), which matures into 28S, 18S and 5.8S rRNAs, which will form the major RNA sections of the ribosome.
- RNA polymerase II synthesizes precursors of mRNAs and most snRNA and microRNAs. This is the most studied type, and, due to the high level of control required over transcription, a range of transcription factors are required for its binding to promoters.
- RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol.
- RNA polymerase IV synthesizes siRNA in plants.
- RNA polymerase V synthesizes RNAs involved in siRNA-directed heterochromatin formation in plants.
Eukaryotic chloroplasts contain an RNAP very highly similar to bacterial RNAP (“plastid-encoded polymerase, PEP”). They use sigma factors encoded in the nuclear genome.
Chloroplast also contain a second, structurally and mechanistically unrelated, single-subunit RNAP (“nucleus-encoded polymerase, NEP”). Eukaryotic mitochondria use POLRMT (human), a nucleus-encoded single-subunit RNAP. Such phage-like polymerases are referred to as RpoT in plants.
How RNA Polymerase Works
RNAP is an abundant enzyme that catalyzes the phosphodiester bonds linking nucleotides by hydrolyzing pyrophosphate from nucleoside triphosphates to form a linear mRNA chain. The growing RNA chain is extended one nucleotide at a time in the 5’→3’ direction using nucleoside triphosphates (ATP, CTP, UTP, and GTP).
Unlike DNA polymerase, RNAP has increased infidelity. On average, one error is made every 10,000 nucleotides. RNAP has a proofreading mechanism to find and replace the wrongly incorporated ribonucleotide and replacing them with the correct one.
Function of RNA Polymerase
RNAP is an important enzyme that initiates transcription in both prokaryotes and eukaryotes. It induces specific DNA sequences on the DNA strand known as a promoter to initiate transcription.
RNA Pol can produce complementary RNA chains to the template DNA strand and can add up to 2.4 million nucleotides in eukaryotes in a process called elongation.
RNA polymerase can produce the following RNA products:
- mRNA (messenger RNA) that translates into proteins.
- RNA genes or non-coding RNA that produce RNA strands, which do not encode proteins but take part in other activities. They include:
- tRNA (transfer RNA) that adds amino acids to the growing polypeptide chain in the process of translation.
- rRNA (ribosomal RNA) is a component of the ribosomes that takes part in translation.
- miRNA (microRNA) regulates gene activity.
- Ribozymes are enzymatically active RNA molecules.
RNA Polymerase vs. DNA Polymerase
RNA polymerase differs from DNA polymerase in many ways:
| Difference | DNA polymerase | RNA polymerase |
| Synthesize | DNA | RNA |
| Activity | Polymerization and proofreading | Only polymerization |
| Process | Involved in replication | Involved in transcription |
| Nucleotides | A, T, G and C | A, U, G and C |
| Cell division | During S1 phase | During G1 and G2 phase |
| Additional enzyme | Helicase and topoisomerase | Holoenzyme |
| Error rate | Very low (due to proof-reading activity) | Very high |
| Speed of polymerization | High | Low |
| Efficiency | High | Low |
| Process | Not de novo | De novo |
| Primer | Required | Not required |