RNA polymerase

RNAP from T. aquaticus pictured during elongation. Portions of the enzyme were made transparent so as to make the path of RNA and DNA more clear. The magnesium ion (yellow) is located at the enzyme active site

RNA polymerase (RNAP or RNApol) is an enzyme responsible for making RNA from a DNA or a RNA template. In all cells RNAP is needed for constructing RNA chains from a DNA template, a process termed transcription. In scientific terms, RNAP is a nucleotidyl transferase that polymerizes ribonucleotides at the 3' end of an RNA transcript. RNA polymerase enzymes are essential and are found in all organisms, cells, and many viruses.

RNAP was discovered independently by Sam Weiss and Jerard Hurwitz in 1960. By this time the 1959 Nobel Prize in Medicine had been awarded to Severo Ochoa for the discovery of what was believed to be RNAP, but instead turned out to be a ribonuclease. The 2006 Nobel Prize in Chemistry was awarded to Roger Kornberg for creating detailed molecular images of RNA polymerase in various stages of transcription.

Control of transcription

File:Transcription label fromcommons.jpg

An electron-micrograph of DNA strands decorated by hundreds of RNAP molecules too small to be resolved. Each RNAP is transcribing an RNA strand which can be seen branching off of the DNA. "Begin" indicates the 5' end of the DNA, where RNAP initiates transcription; "End" indicates the 3' end, where the longer RNA molecules are almost completely transcribed.

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 Escherichia 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 the RNA molecule produced will serve a purely regulatory role to control future gene expression (as seen in siRNA or RNA editing).

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 helicase activity, therefore no separate enzyme is needed to unwind DNA.

RNA polymerase in bacteria

In bacteria, the same enzyme catalyzes the synthesis of three types of RNA: mRNA, rRNA and tRNA.

RNAP is a relatively large molecule. The core enzyme has 5 subunits (~400 kDa):

• α₂: the two α subunits assemble the enzyme and recognize regulatory factors. Each subunit has two domains: αCTD (C-Terminal domain) binds the UP element of the extended promoter, and αNTD (N-terminal domain) binds the rest of the polymerase.
• β: this has the polymerase activity (catalyzes the synthesis of RNA) which includes chain initiation and elongation.
• β': binds to DNA (nonspecifically).
• ω: restores denatured RNA polymerase to its funtional form in vitro. It has been observed to offer a protective/chaperone function to the β' subunit in Mycobacterium smegmatis. Now known to promote assembly.

In order to bind promoter-specific regions, the core enzyme requires another subunit, sigma (σ). The sigma factor greatly reduces the affinity of RNAP for nonspecific DNA while increasing specificity for certain promoter regions, depending on the sigma factor. That way, transcription is initiated at the right region. The complete holoenzyme therefore has 6 subunits: α₂ββ'σω (~480 kDa). The structure of RNAP exhibits a groove with a length of 55 Å (5.5 nm) and a diameter of 25 Å (2.5 nm). This groove fits well the 20 Å (2 nm) double strand of DNA. The 55 Å (5.5 nm) length can accept 16 nucleotides.

When not in use RNA polymerase binds to low affinity sites to allow rapid exchange for an active promoter site when one opens. RNA polymerase holoenzyme, therefore, does not freely float around in the cell when not in use.

Transcriptional cofactors

There are a number of proteins which can bind to RNAP and modify its behavior. For instance, greA and greB from E. coli can enhance the ability of RNAP to cleave the RNA template near the growing end of the chain. This cleavage can rescue a stalled polymerase molecule, and is likely involved in proofreading the occasional mistakes made by RNAP. A separate cofactor, Mfd, is involved in transcription-coupled repair, the process in which RNAP recognizes damaged bases in the DNA template and recruits enzymes to restore the DNA. Other cofactors are known to play regulatory roles, i.e. they help RNAP choose whether or not to express certain genes.

RNA polymerase in eukaryotes

Essential Subunit Of Human RNA Polymerases I, II and III

Eukaryotes have several types of RNAP:

• RNA polymerase I synthesizes a pre-rRNA 45S, 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. 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. For detail of RNA polymerase function see RNA polymerase II.
• RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol.
• Other RNA polymerase types in mitochondria and chloroplasts.

RNA polymerase in archaea

Archaea have a single RNAP that is closely related to the three main eukaryotic polymerases. Thus, it has been speculated that the archaeal polymerase resembles the ancestor of the specialized eukaryotic polymerases.

RNA polymerase in viruses

T7 RNA polymerase producing a mRNA (green) from a DNA template. The protein is shown as a purple ribbon. Image derived from PDB 1MSW.

Many viruses also encode for RNAP. Perhaps the most widely studied viral RNAP is found in bacteriophage T7. This single-subunit RNAP is related to that found in mitochondria and chloroplasts, and shares considerable homology to DNA polymerase. It is believed by many that most viral polymerases therefore evolved from DNA polymerase and are not directly related to the multi-subunit polymerases described above.

The viral polymerases are diverse, and include some forms which can use RNA as a template instead of DNA. This occurs in negative strand RNA viruses and dsRNA viruses, both of which exist for a portion of their life cycle as double-stranded RNA. However, some postive strand RNA viruses, such as polio, also contain these RNA dependent RNA polymerases.

Isolation

RNA polymerase can be isolated in the following ways:

• By a phosphocellulose column (PC).
• By glycerol gradient centrifugation (GG).
• By a DNA column (A).
• By an Ion exchange column.
• PC+A

See also

• DNA polymerase
• T7 RNA polymerase
• Alpha-amanitin

External links

• DNAi - DNA Interactive, including information and Flash clips on RNA Polymerase.