DNA Polymerase II, often referred to as Pol II, represents a specific enzyme found in prokaryotic organisms, such as bacteria like Escherichia coli. This protein belongs to the broader family of DNA polymerases, which are molecular machines responsible for synthesizing DNA. While other polymerases handle the bulk of DNA replication, Pol II plays an important role in safeguarding the cell’s genetic information. Its functions become particularly significant when the bacterial genome faces damage or stress.
The Repair and Restart Function of DNA Polymerase II
DNA Polymerase II primarily functions not in the routine, high-speed duplication of the entire genome, but in specialized repair processes. One of its main responsibilities involves restarting stalled replication forks. When the main replication machinery, DNA Polymerase III, encounters damage or a blockage on the DNA template, it can halt, leaving the replication process incomplete. Pol II is then recruited to help the cell bypass these problematic regions, allowing DNA synthesis to resume.
Pol II can perform translesion synthesis (TLS), synthesizing new DNA across damaged templates. This ability allows the cell to tolerate lesions that would otherwise completely block replication, ensuring that the genome can still be copied, though sometimes with a higher chance of introducing errors.
Distinguishing DNA Polymerase II from Polymerase I and III
Understanding the distinct roles of DNA Polymerase I, II, and III helps clarify their individual contributions within a bacterial cell. DNA Polymerase III is the primary replicative enzyme, responsible for synthesizing the vast majority of new DNA during cell division. It operates with high speed, capable of adding approximately 1,000 nucleotides per second, and exhibits high processivity, meaning it can add many nucleotides without detaching from the DNA template.
DNA Polymerase I, in contrast, primarily removes the RNA primers that initiate DNA synthesis and fills in the resulting gaps with DNA. This enzyme possesses a unique 5′ to 3′ exonuclease activity, a feature not found in Pol II or Pol III. Pol I operates at a slower pace, adding around 100-200 nucleotides per second, and has lower processivity compared to Pol III.
DNA Polymerase II operates at an even lower speed, adding only 1-10 nucleotides per second, and also has low processivity. While Pol III is the high-speed elongator and Pol I handles primer removal and gap filling, Pol II’s specific function lies in its ability to manage DNA damage and restart stalled replication. All three polymerases possess 3′ to 5′ exonuclease activity, which allows them to proofread and correct newly added nucleotides.
Structural Composition of DNA Polymerase II
DNA Polymerase II in E. coli is encoded by the polB gene. It is composed of a single polypeptide chain, making it a monomeric protein. This protein folds into distinct functional regions.
The enzyme’s structure is often described using a “right hand” analogy, featuring palm, fingers, and thumb domains. The palm domain contains catalytic residues that coordinate with metal ions to facilitate DNA synthesis. The fingers and thumb domains are involved in binding the DNA template and positioning it correctly within the active site. Pol II can also interact with accessory proteins, such as the beta-clamp and clamp-loading complex, which enhance its processivity and fidelity during DNA repair.
Induction During the SOS Response
The activity of DNA Polymerase II is closely linked to the SOS response, an emergency system activated by bacteria when they encounter extensive DNA damage. Under normal cellular conditions, the levels of Pol II are relatively low. However, when the bacterial chromosome experiences significant damage, for instance from ultraviolet radiation or certain chemical agents, the SOS response is initiated.
This damage leads to the formation of single-stranded DNA, which activates the RecA protein. Activated RecA then facilitates the self-cleavage of LexA, a repressor protein that normally keeps SOS genes, including polB, turned off. With LexA inactivated, the genes are expressed, leading to a significant increase in the production of Pol II and other repair proteins. This induction ensures the cell has sufficient resources to address widespread DNA damage, aligning Pol II’s specialized repair functions with cellular needs.