RNA Polymerase: Function and Definition

Ribonucleic Acid (RNA) polymerase is an intermediary enzyme responsible for processing gene sequences into RNA-based genetic material that can be utilized in protein synthesis. In this article, we define RNA polymerase and further explore its various functions throughout cell biology.

RNA polymerase is a multi-unit enzyme that synthesizes RNA molecules from a template of DNA through a process called transcription. The transcription of genetic information into RNA is the first step in gene expression that precedes translation, the process of decoding RNA into proteins. The RNA molecules produced by RNA polymerase fulfill a variety of roles in the cell. 

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.

RNA polymerase in action

The three stages of transcription involve various functions of RNA polymerase that result in the synthesis of RNA:

1. 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 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 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.

While prokaryotes like bacteria have one RNA polymerase that transcribes all types of RNA, eukaryotes like plants and mammals can have numerous forms of RNA polymerase.

RNA polymerase I

RNA polymerase I² is responsible for synthesizing most ribosomal RNA (rRNA) transcripts. These transcripts are produced within the nucleolus, a region within the nucleus where ribosomes are assembled. The availability of rRNA molecules produced by RNA polymerase can impact essential functions of cell biology since these transcripts are directly involved with the production of ribosomes.

RNA polymerase II

RNA polymerase II³ transcribes protein-coding genes into messenger RNA (mRNA). This 12-subunit enzyme works as a complex that directly influences gene expression through its production of pre-mRNA transcripts. Once the pre-mRNAs are released by RNA polymerase II within the nucleus, biochemical modifications prepare these transcripts for translation. RNA polymerase II also produces micro RNA (miRNA) molecules. These non-coding transcripts can mediate gene expression and the activity of mRNAs after transcription.

RNA polymerase III

RNA polymerase III² transcribes rRNA genes into small RNAs like transfer RNA (tRNA) and 5S rRNA. These smaller RNA transcripts play a role in normal cell function throughout the nucleus and cytoplasm.

RNA polymerase IV and V

Exclusively found in plants, RNA polymerase IV and V are transcription enzymes that evolved as specialized forms of RNA polymerase II⁴. Both enzymes produce small interfering RNA (siRNA) transcripts, which play a role in the silencing of plant genes.

DNA polymerase synthesizes double-stranded DNA molecules from unwound DNA strands during replication. Even though the end products of replication and transcription are different, they both work on DNA by adding nucleotides in the same 5’ to 3’ direction. In contrast with RNA polymerase, DNA polymerization is a semi-conserved process that utilizes both strands of a double-stranded DNA molecule as a template for replication.

Comparison	RNA Polymerase	DNA Polymerase
Function	Transcription of DNA	Replication of DNA
Purpose	To make RNA copies of genes	To copy the entire genome
Time of occurrence	Used in transcription during G phase(s)	Used in replication during S phase
Primer	Not required for transcription	Required for initiation of replication
Base pairs used to synthesize product	Adenine, Guanine, Cytosine and Uracil	Adenine, Guanine, Cytosine and Thymine
Resulting product	Single-stranded RNAs (e.g. mRNA)	Double-stranded DNAs

RNA polymerase is an attractive target for drug development due to its ubiquitous presence and function throughout life. The biochemical differences in RNA polymerase between prokaryotes and eukaryotes allow for specific drugs that target microbial RNA polymerases without any interaction with our own.

Several antimicrobial drugs function as RNA polymerase inhibitors by blocking bacterial or viral enzyme activity during one stage of transcription. For example, the rifamycins⁵ are a group of bacterial antibiotics that inhibit elongation by blocking the exit channel of RNA polymerase. These drugs are commonly used to treat challenging infections caused by leprosy and tuberculosis.