RNA Polymerase: Properties, Structure, Types, Functions

RNA polymerase is a multi-unit enzyme that synthesis RNA molecules from the DNA molecule during the process of transcription.

• It is responsible for transcribing the genes encoded in DNA molecules into code-able sequences RNA, which further helps during protein synthesis.
• RNA polymerase plays a vital role in transcription, where it attaches itself to the promoter regions of DNA and initiates the process of transcription. Furthermore, this enzyme also adds ribonucleotides and grows the chain of RNA by using the DNA as a template. Moreover, it also terminates the process if it encounters termination sequences in the template DNA.
• RNA polymerase catalyzes the formation of phosphodiester bonds by adding ribonucleoside triphosphates (NTPs) onto the growing chain of new strands. 
• It uses the DNA template to build a polynucleotide with complementary base pairs.
• The free nucleotides U pair with T in the DNA template, G pairs with C in the DNA template.

Properties

• RNA polymerase reads the template DNA as 3′ to 5′ but synthesis the polynucleotide in a 5′ to 3′ direction.
• RNA polymerase does not have nucleases activities so can’t proof-read as DNA polymerase does.
• It does not require a primer to initiate the adding of incoming ribonucleotides.
• In a prokaryotic cell, a single species of RNA polymerase is present. However, the eukaryotic cell requires different RNA polymerase for synthesizing different RNAs. 
• Additionally, eukaryotic RNA polymerase requires many other proteins to initiate transcription, whereas prokaryotic RNA polymerase binds directly to the promoter regions in DNA.

Eukaryotic RNA Polymerase Mechanism

• The major difference in the working mechanism of Eukaryotic RNA polymerase and Prokaryotic RNA polymerase is that eukaryotic RNA polymerase cannot initiate the process of transcription all by itself but prokaryotic RNA polymerase can.
• The eukaryotic RNA polymerase needs additional proteins in order to perform its functions, these additional proteins are referred to as transcription factors.
• Promoter regions of genes that are transcribed by RNA polymerase have a sequence that is similar to the TATA box of 25-30 nucleotides, just a little bit upstream from the transcription initiation site.
• To this sequence of 25-30 nucleotides, transcription factor TFΙΙD binds.
• TFΙΙD itself is a multi-subunit compound, which provides a binding site for another transcription factor called TFΙΙB, forming a complex at the promoter region.
• This complex serves as a bridge for the binding of RNA polymerase.
• This binding of RNA polymerase to the complex at the promoter region is facilitated by another transcription factor called TFΙΙF.
• Following the recruitment of RNA polymerase to the promoter region, additional transcription factors TFΙΙE TFΙΙH are required to initiate transcription.
• TFΙΙH is a multi-subunits factor that acts as a helicase to unwind the double-stranded DNA to make the transcribing of genes possible. This factor also acts as a kinase that phosphorylates RNA polymerase, making it break away from the initiation complex and thus letting the RNA polymerase run along the DNA template to synthesize chains of RNAs, we now enter elongation.
• Elongation is characterized by the addition of ribonucleoside triphosphate (rNTP) via the formation of phosphodiester bond and release of pyrophosphates molecules, this reaction is catalyzed by two divalent metal ions namely:  Magnesium ion and Manganese ion.
• Magnesium ion is responsible for bringing the 3’OH group of the primer to close proximity with a phosphate atom of incoming rNTP.
• Due to which the 3′ free hydroxyl group of primer now nucleophilically attacks a phosphate atom of the triphosphate group of incoming rNTPs and forms a phosphodiester bond.
• As a bond is formed, there is a significant charge developed on the oxygen that was preciously bonded with phosphate atom, and to stabilize this charge manganese ion plays a vital role. Additionally, manganese ion also assists in the departure of the pyrophosphate groups.
• The template of DNA contains a terminal sequence, which marks the termination of the transcription process, the result of which is chains of RNAs. This terminal sequence usually contains 40 nucleotides and is the GC-rich stretch usually ending in six or seven A.
• However, the termination can also happen by cleaving off the growing chains of RNA from RNA polymerase by the action of a hexamer protein called rho. 

Prokaryotic RNA Polymerase Mechanism

• Unlike eukaryotic RNA polymerase, prokaryotic RNA polymerase directly attaches to the promoter regions in the DNA without the assistance of any transcription factors.
• RNA polymerase holoenzyme binds with promoter region and unwinds the DNA strands and begins the synthesis of RNA.
• RNAs are synthesized in the 5′ to 3′ direction by reading the template of DNA in the 3′ to 5′ direction.
• Elongation is characterized by the addition of ribonucleoside triphosphate (rNTP) via the formation of phosphodiester bond and release of pyrophosphates molecules, this reaction is catalyzed by two divalent metal ions namely:  Magnesium ion and Manganese ion.
• Magnesium ion is responsible for bringing the 3’OH group of the primer to close proximity with a phosphate atom of incoming rNTP.
• Due to which the 3′ free hydroxyl group of primer now nucleophilically attacks a phosphate atom of the triphosphate group of incoming rNTPs and forms a phosphodiester bond.
• As a bond is formed, there is a significant charge developed on the oxygen that was preciously bonded with phosphate atom, and to stabilize this charge manganese ion plays a vital role. Additionally, manganese ion also assists in the departure of the pyrophosphate groups.
• The template of DNA contains a terminal sequence, which marks the termination of the transcription process, the result of which is chains of RNAs. This terminal sequence usually contains 40 nucleotides and is a GC-rich stretch usually ending in six or seven A.
• However, the termination can also happen by cleaving off the growing chains of RNA from RNA polymerase by the action of a hexamer protein called rho. 

Structure of Prokaryotic RNA Polymerase

• RNA polymerase in a prokaryotic cell is composed of five polypeptide subunits: an alpha (α) subunit, a beta (β)subunit, a beta prime (β’) subunit, an omega (ω) subunit, and a sigma (σ) subunit.
• The polymerase is a multi-subunits holoenzyme. 
• The first step in the making of RNA polymerase is the dimerization of the alpha subunit (α) and acts as a scaffold to bring two other subunits: beta (β)subunit and beta prime (β’) subunit. One of the alpha subunits interacts with the beta (β)subunit while the other alpha subunit (α) interacts with the beta prime (β’) subunit.
• beta (β)subunit is the prime subunit that has polymerase activity and synthesizes new RNA molecules along with the template of DNA. 
• beta prime (β’) subunit binds to the DNA and also coordinates metal ions for their catalytic activities.
• (ω) subunit is the smallest of all, and is involved in the assembly of holoenzyme and maintaining the structural integrity of the polymerase. 
• And finally, the sigma (σ) subunit is crucial in the recognition of the promoter region in the DNA to initiate the process of transcription.
• However, the catalytic core comprises of α β β’ ω and the sigma (σ) subunit only associate with the core during the recognition of promoter region in the DNA template.
• Once the initiation site is determined, the sigma (σ) subunit dissociates from the catalytic core.

Structure of Eukaryotic RNA Polymerase

• The eukaryotic cell contains three types of distinct RNA polymerases that are involved in the synthesis of different types of RNAs having their own specific functions.
• RNA polymerase Ι transcribe genes that yield rRNAs. 
• RNA polymerase ΙΙ transcribes protein-coding genes and results in the synthesis of mRNAs.
• RNA polymerase ΙΙΙ transcribe genes that yield tRNAs.
• All of these three are complex multi-subunits enzymes consisting of 8-14 subunits each.
• Although they recognize different promoters and transcribe different RNAs, they mostly share common features.
• Even the two largest subunits of eukaryotic RNA polymerase are closely related to β and β’ subunits of prokaryotic RNA polymerase.
• Additionally, these three types of eukaryotic RNA polymerases have five similar subunits in their structures.
• The specificity in these three polymerases is determined by the interactions they have with different other proteins, also referred to as transcriptional factors.
• Eukaryotic RNA polymerases cannot bind to the promoter region of DNA directly like prokaryotic RNA polymerase do, therefore they need these transcription factors in order to bind to DNA and initiate the synthesis of RNAs.
• The different transcription factors involved in the synthesis of different types of RNAs are pivotal in determining the type of RNA polymerase required.
• RNA polymerase structurally is broadly divided into two subunits, a larger subunit and a second large subunit that act coherently to transcribe respective genes.
• The length of these subunits is different in all these three RNA polymerases discussed.
• For instance, RNA polymerase ΙΙ contains 11 cleft loops in two subunits, each loop has a specific length of amino residues. Hence, the variation in the length of amino acid residues in each cleft loop is what separates one polymerase from the other. 

Types and Functions

The major function of RNA polymerase is to transcribe a specific gene in the DNA and synthesize RNA. This synthesis is characterized by the unwinding of that specific portion of the DNA and taking it as a template to transcribe the gene-directed RNAs.

1. RNA polymerase Ι

• This enzyme is responsible for synthesizing ribosomal RNA.
• It transcribes the gene in the nucleolus and synthesizes the rRNA in the nucleus itself, from where it is transported to cytoplasm via either nuclear pore or by carrier proteins, where it forms ribosomes
• Availability of rRNA molecules produced by RNA polymerase 1 can impact important functions in our body, as rRNA is the structural unit of the ribosome, which in turn is a site for protein synthesis.

2. RNA polymerase ΙΙ

• This enzyme is responsible for synthesizing messenger RNA.
• It transcribes proteins coding genes from the DNA into suitable mRNAs that can further be processed to take part in translation.
• The working of this enzyme directly influences the proteins that are to be synthesized, if improper transcription of genes, then would lead to translation of faulty proteins, which can have a severe impact on our body.

3. RNA polymerase ΙΙΙ

• This enzyme is responsible for synthesizing transfer RNA.
• tRNA is responsible for attaching amino acids and making a polypeptide chain as per the codons present in mRNA molecule during protein synthesis.

4. RNA polymerase is an attractive target for pharmaceutical drugs, due to its ubiquitous nature and various functions throughout the life of the cell. Moreover, the biochemical difference in eukaryotic and prokaryotic RNA polymerase, allows specific drugs to target only prokaryotic cells, without interfering with our own cells.
5. With advancements in molecular studies and molecular techniques, the activity of RNA polymerase can be altered by modifying their subunits or general transcription factors involved, to synthesize required RNA.

RNA Polymerase FAQs

References

1. Structure and mechanism of the RNA Polymerase II transcription machinery (nih.gov)
2. Eukaryotic RNA Polymerases and General Transcription Factors – The Cell – NCBI Bookshelf (nih.gov)
3. Transcription and RNA polymerase – An Introduction to Genetic Analysis – NCBI Bookshelf (nih.gov)
4. RNA Polymerase: Function and Definition | Technology Networks
5. metabolism – Synthesis of DNA | Britannica
6. 8.2: Prokaryotic Transcription – Biology LibreTexts
7. Prokaryotic Transcription | Biology for Majors I (lumenlearning.com)
8. An Introduction to the Structure and Function of the catalytic core enzyme of Escherichia coli RNA polymerase (nih.gov)
9. Structural differentiation of the three eukaryotic RNA polymerases – ScienceDirect