RNA Polymerase: Check Structure, Types and Function

RNA Polymerase is an essential enzyme that makes RNA from DNA during the process of transcription. It was discovered in the 1950s by scientists, Samuel Weiss and Jerard Hurwitz. It enables the transfer of genetic information from DNA to RNA and ensures the correct sequence is formed to avoid any mutations. This enzyme plays a key role in the molecular basis of inheritance.

This Story also Contains

1. What Is RNA Polymerase?
2. Structure Of RNA Polymerase
3. Functions Of RNA Polymerase
4. Components Of RNA Polymerase
5. RNA Polymerase And Disease
6. Experimental Techniques To Study RNA Polymerase
7. Recommended video for "RNA Polymerase"
8. MCQs on RNA Polymerase

RNA polymerase reads DNA and produces complementary RNA strands based on the genetic code. It performs the same reaction in all cells, from bacteria to humans. Bacteria have single RNA polymerase whereas eukaryotes have three: RNA polymerase I, II, and III. It is necessary to understand the function of RNA polymerase, as it has applications in various fields like genetics, biotechnology, and research.

What Is RNA Polymerase?

RNA polymerase is an important enzyme which synthesises RNA from a DNA template during. It reads the DNA sequence and produces the mRNA sequence, which either goes on to make proteins or performs other cellular functions. This enzyme first unwinds the double helix DNA and then forms mRNA, based upon the complementary DNA sequence.

Without RNA polymerase, cells will not be able to transcribe the genetic information in the DNA and make proteins that will perform vital cellular functions. It helps cells to transcribe genes as needed to ensure proper functioning and respond to the changes in the environment. The process is necessary and vital for growth, development, and general adaptation in the living body.

Structure Of RNA Polymerase

RNA polymerase has multiple subunits. It consists of a collection of protein subunits that perform the activities of an enzyme. In prokaryotes, the core polymerase comprises five subunits: two alpha, one beta, one beta prime, and one omega. The enzyme consists of three subunits—β and β', which together form the catalytic centre, and α, which is involved in assembly and regulation.

Comparison Of Prokaryotic And Eukaryotic RNA Polymerase

Prokaryotic RNA Polymerase is less complicated than eukaryotic ones. Prokaryotes have a single RNA polymerase that synthesizes all the types of RNA whereas eukaryotes have three distinct RNA polymerases.

Prokaryotic RNA Polymerase (Core Enzyme, Sigma Factor)

In prokaryotic cells RNA Polymerase needs an additional subunit called the sigma (σ) factor for initiation of transcription. This σ factor binds to specific promoter regions on the DNA and allows the binding of the core enzyme to start RNA synthesis.

Eukaryotic RNA Polymerase (Types I, II, and III)

Eukaryotes have three different types of RNA Polymerase, each transcribing different type of RNA: The three types are:

• RNA polymerase I transcribes rRNA genes.

• RNA polymerase II transcribes mRNA and some snRNAs.

• RNA polymerase III transcribes tRNA, 5S rRNA, and other small RNAs.

These differences show the greater complexity and specialisation of eukaryotic cells compared to that of prokaryotes.

Functions Of RNA Polymerase

RNA polymerase reads the DNA sequence and forms a complementary strand of RNA. The function of RNA Polymerase include:

Role In Transcription

• Initiation: The binding of RNA Polymerase to the promoter region of a gene by several transcription factors, initiates transcription.

• Elongation: The enzyme moves along the DNA template, synthesizing RNA by adding nucleotides matching the DNA sequence.

• Termination: The process ends with the termination signal, and when the RNA Polymerase reaches a termination site, the newly synthesised RNA is released from the template.

RNA Synthesis

The mechanism of RNA synthesis goes through the following steps:

• RNA Polymerase binds to DNA at the promoter.

• The enzyme unwinds the DNA helix forming transcription bubble.

• Ribonucleotides are joined together in a continuous RNA strand.

• The RNA strand continues to grow in length until a termination signal is reached.

• The RNA molecule is released and the double helix structure of the DNA is restored.

Components Of RNA Polymerase

RNA polymerase is a multi subunit enzyme that works together to perform the process of transcription. The components vary depending on the type of organisms. Each component has a specific role, they ensure proper initiation and elongation of the RNA strand. The components of RNA Polymerase in different organisms are:

Bacteria

The core enzyme of bacterial RNA Polymerase has a composition of five subunits: two alpha subunits, one beta subunit, one beta prime subunit, and one omega subunit.

Alpha (α) Subunits: Assembly of the enzyme and contact with the regulatory proteins. Each α subunit is composed of two domains, an N-terminal domain (NTD), and a C-terminal domain (CTD). CTD can interact with DNA and transcription factors.

Beta and Beta Prime Subunits (β and β'): They form the catalytic centre wherein the RNA synthesis takes place. The β subunit mainly forms the phosphodiester bonds between nucleotides. Meanwhile, the β' subunit also has a role in DNA binding.

Omega Subunit (ω): This provides stability to the whole RNA Polymerase complex and helps the assembly of its core enzyme.

Sigma Factor (σ): The σ factor is required for initiation of transcription. This factor instructs RNA Polymerase to find a promoter site on the DNA and bind on it. It also helps the enzyme to initiate synthesis at the correct location on the RNA.

Multiple σ factors exist in the bacteria, each recognizing different sets of promoters that enable the bacteria to distinguish between a variety of environmental conditions and stresses.

Eukaryotes

Eukaryotic cells contain three main types of RNA Polymerase, each specialized to transcribe different classes of genes. Eukaryotic RNA Polymerases are far from simple and need many more factors to generate the initiation complex.

1. RNA Polymerase I: Transcribes most ribosomal RNA genes - in particular, 5.8S, 18S, and 28S rRNA. This enzyme is localised within the nucleolus.

Subunits: The enzyme consists of 14 subunits. Some of these represent eukaryotic homologues of bacterial RNA Polymerase subunits.

2. RNA Polymerase II: Transcribes messenger RNA, specialised for protein-encoding messages, and a few small nuclear RNAs. It is mainly involved in splicing.

Subunits: It contains 12 subunits. The largest subunit has a C-terminal domain at the end with repeating heptapeptide sequences at the end, which are phosphorylated and therefore play a significant role in transcriptional regulation.

3. RNA Polymerase III: Transcribes transfer RNA, 5S rRNA, and other small RNAs.

Subunits: It is composed of 17 subunits, some of which come only with Pol III, whereas others are shared with Pol I and Pol II.

Archaea

RNA Polymerase of archaea is similar to eukaryotic RNA Polymerase II rather than bacterial RNA Polymerase. It shows the evolutionary history of archaea that is separable from that of bacteria.

Subunits: Contains a lot of subunits (~12-13); most of them have homologs in the eukaryotic RNA Polymerase II. This includes the biggest subunit, Rpo1, which has a homolog to the biggest subunit of RNA Polymerase II, RPB1, and other subunits similar to RPB2, RPB3, etc.

Transcription Factors

Unlike bacteria, archaea do not utilize a σ factor for initiation. They instead rely on eukaryotic TBP and TFB-like transcription factors that recognise and bind to the promoter regions.

TFB and TBP: These factors help recruit the RNA polymerase to the DNA and are hence essential for the assembly of the initiation complex of transcription in archaea.

RNA Polymerase And Disease

Another avenue through which extremely severe activities can arise is mutation of genes encoding subunits or other factors of RNA Polymerase; for instance, many disorders of neurodevelopment have been described due to mutation in the POLR3A-encoded subunit of RNA Polymerase III.

It is also implicated in many diseases, among which is cancer since overexpression or mutations in subunits of RNA Polymerase II are detected in many tumors and can cause aberrant gene expression. Moreover, in viral infections, the host's RNA Polymerase machinery can be hijacked to start the transcription of viral genes at the cost of normal cellular functions.

Experimental Techniques To Study RNA Polymerase

ChIP is also utilised to probe RNA Polymerase–DNA interactions. By using special antibodies recognizing RNA Polymerase or other associated proteins, it becomes possible to find the parts of the DNA bound by them. This shall therefore unfold information on the patterns of transcriptional control.

RNA sequencing has enabled to have information about RNA transcripts in the cell, identifying the genes which, at any specific time, are getting actively transcribed by RNA Polymerase and the information showing the tertiary expression of genes under different conditions.

Gel electrophoresis is used to separate and analyze RNA molecules. It can be used for the assessment of quality and size of RNA transcripts produced by RNA Polymerase, and therefore in the investigation of transcriptional fidelity and processing.

These experimental techniques are critical for the understanding of the function and regulation of RNA polymerase. They allow researchers to dissect complicated interactions and processes related to this enzyme, thus generally enhancing knowledge about gene expression and its impact on health and disease.

Recommended video for "RNA Polymerase"

MCQs on RNA Polymerase

Q1. What is the role of RNA polymerase II in eukaryotic transcription?

1. RNA polymerase II binds to the promoter region and synthesizes mRNA.

2. RNA polymerase II is responsible for the transcription of ribosomal RNA.

3. RNA polymerase II synthesizes small nuclear RNA for splicing of pre-mRNA.

4. RNA polymerase II synthesizes transfer RNA for translation.

Correct Answer: 1) RNA polymerase II binds to the promoter region and synthesizes mRNA.

Explanation:

Explanation of the correct option

Option 1 RNA polymerase II is responsible for synthesizing mRNA in eukaryotic cells. It binds to the promoter region of genes and catalyzes the synthesis of pre-mRNA, which is then processed into mature mRNA. RNA polymerase II is a large complex that requires the assistance of various accessory proteins, including transcription factors and mediator proteins, to properly initiate and regulate transcription.

Incorrect option 2 RNA polymerase II is responsible for the transcription of ribosomal RNA. This is incorrect. RNA polymerase I is primarily responsible for the transcription of ribosomal RNA in eukaryotes.

Incorrect option 3 RNA polymerase II synthesizes small nuclear RNA for splicing of pre-mRNA. This is partially correct. RNA polymerase II transcribes pre-mRNA, which is then processed to remove introns and add a 5' cap and 3' poly-A tail. Small nuclear RNAs (snRNAs) are also transcribed by RNA polymerase II and are involved in the splicing process.

Incorrect option 4 RNA polymerase II synthesizes transfer RNA for translation. This is incorrect. Transfer RNA (tRNA) is transcribed by RNA polymerase III in eukaryotes.

Hence, the correct answer is option 1) RNA polymerase II binds to the promoter region and synthesizes mRNA.

Q2. Statement 1: Prokaryotes use the same RNA polymerase to transcribe all of their genes.

Statement 2: Eukaryotic RNA polymerase III is responsible for the transcription of tRNA, 5srRNA, and snRNAs (small nuclear RNAs).

1. Both statements 1 and 2 are true.

2. Statement 1 is true, but statement 2 is false.

3. Statement 1 is false, but statement 2 is true.

4. Both statements 1 and 2 are false.

Correct answer: 1) Both assertion and reason are true, and the reason is the correct explanation of the assertion.

Explanation:

The assertion is correct. The sigma factor plays an important role in transcription initiation in prokaryotes. In prokaryotic cells, the sigma factor is a subunit of RNA polymerase that recognizes the promoter region of DNA and helps to initiate transcription.

The reason is also correct. The sigma factor recognizes the promoter region of DNA and facilitates the binding of RNA polymerase to initiate transcription. Specifically, the sigma factor recognizes specific DNA sequences known as promoter elements, which are located upstream of the transcription start site. These promoter elements are different in different genes and dictate the specificity of transcription initiation.

Hence the correct answer is option 1) Both assertion and reason are true, and the reason is the correct explanation of the assertion.

Q3. In prokaryotic RNA polymerase ____ subunit binds the DNA template strand.

1. Alpha

2. Beta

3. Delta

4. Gamma

Correct answer: 2) Beta

Explanation:

In prokaryotic organisms, RNA polymerase is a multi-component enzyme, composed of core subunits (α2, β, and β') and a distinctive σ (sigma) factor. The sigma subunit's primary role is to identify the promoter site on DNA, which is essential for initiating transcription. It facilitates the binding of the RNA polymerase to the DNA template, ensuring the precise commencement of the transcription process. After this initial step, the σ subunit typically separates from the complex, allowing the core enzyme to elongate the RNA molecule. In prokaryotic RNA polymerase beta subunit binds the DNA template strand.

Hence, the correct answer is option 2) Beta.

Also Read:

• MCQs in RNA Polymerase in Prokaryotes and Eukaryotes

• Human Genome Project

• Nucleic Acid and Genetic Code