RNA Polymerase

RNA Polymerase Definition

A ribonucleic acid polymerase, or RNA polymerase (RNAP), is a multi subunit enzyme that catalyzes the process of transcription where an RNA polymer is synthesized from a DNA template. The sequence of the RNA polymer is complementary to that of the template DNA and is synthesized in a 5’→ 3′ orientation. This RNA strand is called the primary transcript and needs to be processed before it can be functional inside the cell.

RNA polymerases interact with many proteins in order to accomplish their task. These proteins help in enhancing the binding specificity of the enzyme, aid in unwinding the double helical structure of DNA, modulate the activity of the enzyme based on the requirements of the cell and alter the speed of transcription. Some RNAP molecules can catalyze the formation of a polymer over four thousand bases in length every minute. However, they have a dynamic range of velocities and they can occasionally pause, or even stop at certain sequences in order to maintain fidelity during transcription.

Functions of RNA Polymerase

Traditionally, the central dogma of molecular biology has looked at RNA as a messenger molecule, that exports the information coded into DNA out of the nucleus in order to drive the synthesis of proteins in the cytoplasm: DNA → RNA → Protein. The other well known RNAs are transfer RNA (tRNA) and ribosomal RNA (rRNA) which are also intimately connected with the protein synthetic machinery. However, over the past two decades, it has become increasingly clear that RNA serves a range of functions, of which protein coding is only one part. Some regulate gene expression, others act as enzymes, some are even crucial in the formation of gametes. These are called non-coding or ncRNA.

Since RNAP is involved in the production of molecules that have such a wide range of roles, one of its main functions is to regulate the number and kind of RNA transcripts formed in response to the cell’s requirements. A number of different proteins, transcription factors and signaling molecules interact with the enzyme, especially the carboxy-terminal end of one subunit, to regulate its activity. It is believed that this regulation was crucial for the development of eukaryotic plants and animals, where genetically identical cells show differential gene expression and specialization in multicellular organisms.

In addition, the optimal functioning of these RNA molecules depends on the fidelity of transcription – the sequence in the DNA template strand must be represented accurately in the RNA. Even a single base change in some regions can lead to a completely non-functional product. Therefore, while the enzyme needs to work quickly and complete the polymerization reaction in a short span of time, it needs robust mechanisms to ensure extremely low error rates. The nucleotide substrate is screened at multiple steps for complementarity to the template DNA strand. When the correct nucleotide is present, it creates an environment conducive to catalysis and the elongation of the RNA strand. Additionally, a proofreading step allows incorrect bases to be excised.

Finally, RNA polymerases are also involved in post-transcriptional modification of RNAs to make them functional, facilitating their export from the nucleus towards their ultimate site of action.

Types of RNA Polymerase

There is remarkable similarity in the RNA polymerases found in prokaryotes, eukaryotes, archea and even some viruses. This points to the possibility that they evolved from a common ancestor. Prokaryotic RNAP is made of four subunits, including a sigma-factor that dissociates from the enzyme complex after transcription initiation. While prokaryotes use the same RNAP to catalyze the polymerization of coding as well as non-coding RNA, eukaryotes have five distinct RNA polymerases.

Eukaryotic RNAP I is a workhorse, producing nearly fifty percent of the RNA transcribed in the cell. It exclusively polymerizes ribosomal RNA, which forms a large component of ribosomes, the molecular machines that synthesize proteins. RNA Polymerase II is extensively studied because it is involved in the transcription of mRNA precursors. It also catalyzes the formation of small nuclear RNAs and micro RNAs. RNAP III transcribes transfer RNA, some ribosomal RNA and a few other small RNAs and is important since many of its targets are necessary for normal functioning of the cell. RNA polymerases IV and V are found exclusively in plants, and together are crucial for the formation of small interfering RNA and heterochromatin in the nucleus.

Process of Transcription

Transcription begins with the binding of the RNAP enzyme to a specific part of the DNA, also known as the promoter region. This binding requires the presence of a few other proteins – the sigma factor in prokaryotes and various transcription factors in eukaryotes. One set of proteins called general transcription factors are necessary for all eukaryotic transcriptional activity and include Transcription Initiation Factor II A, II B, II D, II E, II F and II H. These are supplemented by specific signaling molecules that modulate gene expression through stretches of non-coding DNA located upstream. Often initiation is aborted multiple times before a stretch of ten nucleotides is polymerized. After this, the polymerase moves beyond the promoter and loses most of the initiation factors.

This is followed by the unwinding of double stranded DNA, also known as ‘melting’, to form a sort of bubble where active transcription occurs. This ‘bubble’ appears to move along the DNA strand as the RNA polymer elongates. Once transcription is complete, the process is terminated and the RNA strand is processed. Prokaryotic RNAP and eukaryotic RNA polymerases I and II require additional transcription termination proteins. RNAP III terminates transcription when there is a stretch of Thymine bases on the non-template strand of DNA.

Comparison between DNA and RNA Polymerase

While DNA and RNA polymerases both catalyze nucleotide polymerization reactions, there are two major differences in their activity. Unlike DNA polymerases, RNAP enzymes do not need a primer to begin the polymerization reaction. They are also capable of beginning the reaction from the middle of a DNA strand and reading ‘STOP’ signals that cause the enzyme complex to dissociate from the template. Finally, while RNA polymerases are slightly slower that their counterparts, they have the advantage of only needing to make a complementary copy of one strand of DNA.

Related Biology Terms

  • 3′ -> 5′ orientation – Directionality of a single strand of nucleic acid which derives from the numbering of carbon atoms on the nucleotide sugar ring. One end of the nucleic acid has a free hydroxyl group on the third carbon and the other end has a free phosphate group attached to the fifth carbon.
  • Heterochromatin – Segments of a chromosome that are transcriptionally silent and appear to be denser that actively transcribed regions.
  • siRNA – Small interfering RNA are short double stranded RNA molecules involved in gene regulation through RNA interference.
  • Carboxy-terminus – One end of a protein or polypeptide that contains a free carboxyl group attached to the alpha-carbon atom of the amino acid. The other end of the polypeptide is called the N-terminus or amino-terminus.

Quiz

1. Which of these RNA polymerases catalyzes the formation of messenger RNA (mRNA)?
A. RNAP I
B. RNAP II
C. RNAP III
D. RNAP V

Answer to Question #1

2. Which of these RNA polymerases is only found in plants?
A. RNAP I and II
B. RNAP I and III
C. RNAP IV and V
D. None of the above

Answer to Question #2

3. Which of these is present during prokaryotic transcription initiation?
A. Sigma factor
B. Transcription Factor II A
C. Transcription Factor II B
D. Transcription Factor II D

Answer to Question #3
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