Difference Between RNA Polymerase 1, 2 and 3

The main difference between RNA Polymerase 1, 2 and 3 is that the RNA polymerase 1 (Pol 1) transcribes rRNA genes and, the RNA polymerase 2 (Pol 2) mainly transcribes mRNA genes while the RNA polymerase 3 (Pol 3) mainly transcribes tRNA genes.

RNA polymerase is the enzyme involved in the transcription of genes into RNA molecules during the first step of protein synthesis. Meanwhile, eukaryotes have three types of RNA polymerases classified as RNA polymerase 1, 2, and 3 based on the type of RNA they polymerize.

Key Areas Covered

1. What is RNA Polymerase 1
     – Definition, Subunits, Transcription
2. What is RNA polymerase 2
     – Definition, Subunits, Transcription
3. What is RNA Polymerase 3
     – Definition, Subunits, Transcription
4. What are the Similarities Between RNA Polymerase 1, 2 and 3
     – Outline of Common Features
5. What is the Difference Between RNA Polymerase 1, 2 and 3
     – Comparison of Key Differences

Key Terms

RNA Polymerase 1, RNA Polymerase 2, RNA Polymerase 3, Subunits, Types of RNA

What is RNA Polymerase 1

RNA polymerase 1 (Pol 1) is a type of eukaryotic RNA polymerase responsible for the synthesis of pre-rRNA, which is 45S. The maturation of 45S rRNA produces 28S, 18S and 5.8S rRNAs. 28S and 5.8S are the rRNA component of the large subunit while 18S forms the small subunit of the eukaryotic ribosome. RNA polymerase 1 is responsible for the production of 50% of the total RNA of the cell.

Figure 1: Formation of Ribosome from rRNA

RNA polymerase 1 is a 590 kDa enzyme, which contains 14 protein subunits. 10 subunits out of them are involved in the formation of the core: Rpb5, Rpb6, Rpb8, Rpb10, Rpb12, A190, A135, AC40, AC19, and A12.2. The five subunitsRpb5, Rpb6, Rpb8, Rpb10, and Rpb12 also occur in RNA polymerase 2 and 3 as well.

What is RNA Polymerase 2

RNA polymerase 2 (Pol 2) is the main type of RNA polymerase involved in the transcription in eukaryotes. It mainly transcribes the protein–coding genes into mRNA. Apart from that, RNA polymerase 2 transcribes miRNA, snRNA, and snoRNA genes as well.

Figure 2: Role of RNA Polymerase 2

RNA polymerase 2 is a 550 kDa enzyme with 12 protein subunits. The largest subunit of RNA polymerase II consists of a C terminal domain (CTD) of which the phosphorylation is essential for the transcription and RNA processing.

What is RNA Polymerase 3

RNA polymerase 3 is the type of eukaryotic RNA polymerase that mainly transcribes tRNA genes. It also transcribes 5S rRNA genes and U6 spliceosomal RNA genes. The genes that are transcribed by RNA polymerase 3 are housekeeping genes whose function is essential for a living cell. Hence, the expression of RNA polymerase 3 is tightly-regulated during cell growth. The transcription of tRNA genes and 5S rRNA genes are initiated by separate transcription factors.

Figure 3: tRNA Structure

Similarities Between RNA Polymerase 1, 2 and 3

• RNA polymerase 1, 2, and 3 are three types of eukaryotic RNA polymerases.
• They are involved in the transcription of genes into various types of RNA.
• All three RNA polymerases consist of common subunits other than α-like subunits. In addition, each RNA polymerase contains three-seven unique smaller subunits.
• The main function of them is to add complementary RNA nucleotides to a DNA strand. Therefore, all three RNA polymerases are DNA-dependent-RNA polymerases.
• They do not require a primer for the initiation of the polymerization.
• They add RNA nucleotides in the 5’ to 3’ direction, linking them through the formation of phosphodiester bonds.
• The energy for polymerization comes from the hydrolysis of the phosphoanhydride bond between alfa and beta of the incoming nucleotide.

Difference Between RNA Polymerase 1, 2 and 3

Definition

RNA polymerase 1 refers to the RNA polymerase that only transcribes ribosomal RNA (but not 5S rRNA), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell. RNA polymerase 2 refers to the central enzyme that catalyses DNA-directed mRNA synthesis during the transcription of protein-coding genes whereas RNA polymerase 3 refers to the RNA polymerase that transcribes small untranslated RNAs, such as tRNAs.

Types of RNA Transcribed

RNA polymerase 1 transcribes rRNA genes while RNA polymerase 2 transcribes mRNA, miRNA, snRNA, and snoRNA genes. RNA polymerase 3 transcribes tRNA and 5S rRNA genes. This is the main difference between RNA Polymerase 1, 2 and 3.

Location inside the Nucleus

RNA polymerase 1 resides in the nucleolus while RNA polymerase 2 and 3 reside in the nucleoplasm.

Genes

RNA polymerase 1 transcribes pre-rRNA at ~200 copies while RNA polymerase 2 transcribe ~25,000 genes, and RNA polymerase 3 transcribes 30-50 genes at variable copy numbers.

Alpha-like Subunit

RNA polymerase I and III contain the same two non-identical α-like subunits, whereas polymerase II has two copies of a different α-like subunit.

Inhibition with Alpha-Amanitin

RNA polymerase 1 is insensitive to α-amanitin; RNA polymerase 2 is sensitive to 1 μg/mL α-amanitin, and RNA polymerase 3 is sensitive to 10 μg/mL α-amanitin.

Conclusion

RNA polymerase 1 transcribes rRNA genes while RNA polymerase 2 transcribes mRNA genes, and RNA polymerase 3 transcribes tRNA genes. Moreover, RNA polymerase 1 occurs in the nucleolus while RNA polymerase 2 and 3 occur in the nucleoplasm of the nucleus. The main difference between RNA polymerase 1, 2 and 3 is the type of transcribing genes and their location inside the nucleus.

Reference:

1. Tafur, Lucas et al. “Molecular Structures of Transcribing RNA Polymerase I.” Molecular Cell 64.6 (2016): 1135–1143. PMC. Web. 10 July 2018, Available Here
2. Hahn, Steven. “Structure and Mechanism of the RNA Polymerase II Transcription Machinery.” Nature structural & molecular biology 11.5 (2004): 394–403. PMC. Web. 10 July 2018, Available Here
3. Khatter, Heena. RNA Polymerase I and III: Similar Yet Unique. vol. 47, ELSEVIER, Available Here

Image Courtesy:

1. “Ribosomal rRNA subunits” (CC BY 3.0) via Commons Wikimedia
2. “DNA transcription” By reworked and vectorized by myself – National Human Genome Research Institute, (Public Domain) via Commons Wikimedia
3. “The tRNA cloverleaf general” By Yikrazuul – Own work (CC BY-SA 3.0) via Commons Wikimedia