DNA replication in bacteria is carried out by a group of enzymes called DNA polymerases. To understand how cells maintain genetic stability, it is important to study the types of DNA polymerase in prokaryotes and their functions. Prokaryotic organisms, such as E. coli, contain five DNA polymerases—Pol I, Pol II, Pol III, Pol IV, and Pol V. Each has a specific role, from synthesizing new DNA strands to proofreading errors and repairing damaged DNA. This article explains their functions in detail, making it useful for MSc students and CSIR NET preparation.
What is DNA polymerase?
DNA polymerase is an enzyme that synthesizes new DNA strands using an existing DNA template. In prokaryotes such as E. coli, several DNA polymerases work together to copy genetic material during DNA replication.
These enzymes not only build new DNA but also proofread and repair errors, ensuring that the genetic code is passed on accurately to the next generation. Understanding the types of DNA polymerase in prokaryotes and their functions is crucial for microbiology students and exam aspirants.
Different Types of DNA Polymerase in Prokaryotes
Prokaryotes have five main DNA polymerases: Pol I, Pol II, Pol III, Pol IV, and Pol V. Among these, DNA Polymerase III is the primary enzyme of replication, while the others play specialized roles in primer removal, repair, and the SOS response.
A) DNA Polymerase I (Pol I)
- Also known as the Kornberg enzyme.
- Removes RNA primers on the lagging strand.
- Fills gaps with DNA nucleotides.
- Has unique 5′ → 3′ exonuclease activity.
- Plays an important role in Okazaki fragment processing and nick translation.
B) DNA Polymerase II (Pol II)
- Functions mainly in DNA repair.
- Helps restart stalled replication forks.
- Possesses 3′ → 5′ proofreading activity.
- Acts as a backup enzyme during stress.
C) DNA Polymerase III (Pol III) – The Holoenzyme
- The main replicative enzyme in E. coli.
- Has very high processivity due to the sliding β-clamp.
- Synthesizes both leading and lagging DNA strands.
- Provides 3′ → 5′ proofreading for accuracy.
Subunits of DNA Polymerase III Holoenzyme and Their Roles
| Subunit | Role |
|---|---|
| α-subunit | DNA synthesis (polymerase activity) |
| ε-subunit | Proofreading (3′ → 5′ exonuclease) |
| θ-subunit | Stabilizes ε-subunit |
| β-subunit | Sliding clamp → processivity |
| γ-complex | Clamp loader → helps β-clamp attach |
DNA Polymerase IV (Pol IV)
- Member of the Y-family of polymerases.
- Performs translesion synthesis (copies across damaged DNA).
- Error-prone, introducing mutations.
- Active during the SOS response.
DNA Polymerase V (Pol V)
- Works in the SOS repair pathway.
- Copies across thymine dimers and bulky lesions.
- Highly error-prone and mutagenic.
- Provides a survival mechanism under DNA damage.
Comparison Chart: Types of DNA Polymerase in Prokaryotes
| Polymerase | Main Role | Exonuclease Activity | Special Feature |
|---|---|---|---|
| Pol I | Primer removal, gap filling | 5′ → 3′ & 3′ → 5′ | Nick translation |
| Pol II | DNA repair, restart stalled forks | 3′ → 5′ | Repair enzyme |
| Pol III | Major replication enzyme | 3′ → 5′ | High processivity (β-clamp) |
| Pol IV | Translesion synthesis | None | Error-prone, SOS repair |
| Pol V | Mutagenic SOS repair | None | Bypasses thymine dimers |
Exonuclease Activity of DNA Polymerase
Definition:
Exonuclease activity is the ability of DNA polymerase (or other enzymes) to remove nucleotides one at a time from the ends of a DNA strand.
- Exo- means “outside”,
- nuclease means “enzyme that cuts nucleic acids”.
DNA polymerases in prokaryotes may have two types of exonuclease activities:
- 5′ → 3′ Exonuclease activity
- Removes nucleotides from the 5′ end toward the 3′ end.
- Found in DNA Polymerase I.
- Function: Removes RNA primers in Okazaki fragment processing and damaged DNA.
- 3′ → 5′ Exonuclease activity (Proofreading)
- Removes nucleotides from the 3′ end (the growing DNA strand).
- Found in Pol I, Pol II, Pol III.
- Function: Corrects mistakes by removing wrongly inserted bases → ensures high fidelity replication.
Role of Exonuclease Activity
| Type of Exonuclease | Found in | Role | Importance |
|---|---|---|---|
| 3′ → 5′ exonuclease | Pol I, II, III | Proofreading → removes mispaired bases from newly synthesized DNA | Increases accuracy of DNA replication |
| 5′ → 3′ exonuclease | Pol I only | Removes RNA primers and damaged nucleotides ahead of synthesis | Essential for Okazaki fragment maturation and DNA repair |
Example: Proofreading by 3′ → 5′ Exonuclease
If DNA Pol III adds the wrong base (e.g., A opposite G), it stalls.
👉 The 3′ → 5′ exonuclease removes the incorrect base.
👉 Then, DNA polymerase adds the correct base.
✅ This keeps the replication error rate very low (~1 mistake in 10⁷ bases).
Example: Primer Removal by 5′ → 3′ Exonuclease (Pol I)
- On the lagging strand, RNA primers start Okazaki fragments.
- DNA Pol I removes these primers using its 5′ → 3′ exonuclease.
- Then it fills the gap with DNA nucleotides.
- Finally, DNA ligase seals the nick.
🔑 In summary:
- 3′ → 5′ exonuclease = Proofreading → increases fidelity.
- 5′ → 3′ exonuclease = Primer removal + nick translation (Pol I).
DNA Polymerase vs RNA Polymerase
- DNA Polymerase: Uses DNA template to make DNA. Requires a primer.
- RNA Polymerase: Uses DNA template to make RNA. No primer required.
Conclusion: Types of DNA Polymerase in Prokaryotes and Their Functions
Prokaryotes rely on a diverse array of DNA polymerases to manage the crucial processes of DNA replication and repair.
- DNA Polymerase III (Pol III) serves as the primary enzyme for DNA replication. DNA Pol III ensures efficient and processive synthesis of both leading and lagging strands.
- DNA Polymerase I (Pol I) plays a vital role in the removal of RNA primers and filling gaps during replication. Pol I also works during DNA repair.
- DNA Polymerase II (Pol II), along with DNA Polymerase IV (Pol IV) and DNA Polymerase V (Pol V), are essential for specialized repair mechanisms, particularly under stress conditions, contributing to the organism’s ability to bypass damaged DNA sections through translesion synthesis.
This sophisticated system of DNA polymerases is fundamental to maintaining genomic stability, which is critical for the survival and adaptability of prokaryotic organisms. For microbiology students, a thorough understanding of these enzyme functions is essential for success in academic assessments such as MSc and CSIR NET examinations.