DNA replication copies a cell’s genetic blueprint before cell division. This duplication is executed by specialized enzymes known as DNA polymerases, which assemble new DNA strands. DNA Polymerase III (Pol III) is the primary engine for this undertaking in bacteria, such as E. coli. Pol III’s function explains how cells duplicate their vast genomes with speed and accuracy.
The Primary Role in DNA Elongation
Pol III’s primary task is the rapid synthesis of new DNA chains, a process called elongation. It reads the original template strand and incorporates complementary nucleotides to build the new strand. This enzyme synthesizes DNA strictly in the 5′ to 3′ direction.
Because DNA strands are anti-parallel, Pol III handles the two template strands differently at the replication fork. It synthesizes the leading strand continuously toward the fork as the DNA unwinds. For the lagging strand, Pol III works in reverse, building the new DNA in short segments known as Okazaki fragments.
Pol III cannot begin synthesis from scratch. It requires a short existing segment called an RNA primer, which is synthesized by the enzyme primase. This primer provides a starting point with a free 3′-hydroxyl group.
The Holoenzyme Structure and Processivity
Pol III achieves its speed and efficiency as a large, multi-subunit complex known as the DNA Polymerase III holoenzyme. This complex structure allows Pol III to add thousands of nucleotides without detaching from the DNA strand.
The core of this efficiency is the ring-shaped accessory factor called the beta (\(\beta\)) clamp, or sliding clamp. The clamp is formed by two identical protein subunits that encircle the DNA double helix. This ring physically tethers the Pol III core enzyme to the template strand, preventing the polymerase from diffusing away.
This tethering is the source of Pol III’s high processivity, which measures how many nucleotides an enzyme can add before it falls off the template. By being clamped onto the DNA, Pol III can synthesize DNA at rates up to 1,000 nucleotides per second in E. coli. The beta clamp must be loaded onto the DNA by the clamp loader complex, which opens and closes the ring.
Ensuring Accuracy Through Proofreading
DNA Polymerase III maintains high accuracy in copying the genetic code through an intrinsic quality control mechanism called proofreading. This function is carried out by a separate enzymatic activity within the holoenzyme complex.
Pol III possesses 3′ to 5′ exonuclease activity, which is distinct from its 5′ to 3′ polymerization activity. If the enzyme incorporates an incorrect nucleotide, the mismatch causes a distortion that stalls the polymerase. The enzyme then shifts the newly synthesized strand into a second active site.
This secondary site, located on the epsilon (\(\epsilon\)) subunit, acts as a molecular eraser. The 3′ to 5′ exonuclease activity removes the incorrectly paired nucleotide from the growing chain’s 3′ end. Once the error is excised, the DNA strand moves back to the polymerization site, and Pol III inserts the correct base to continue synthesis.
How Pol III Differs from Other Polymerases
Although Pol III handles the bulk of replication, it does not work in isolation; bacteria contain several other DNA polymerases with specialized functions. The most notable difference is between Pol III and DNA Polymerase I (Pol I), which plays a complementary role in replication cleanup.
Pol I is involved in DNA repair and processing the lagging strand’s Okazaki fragments. It possesses a unique 5′ to 3′ exonuclease activity that Pol III lacks. Pol I uses this activity to remove the RNA primers that initiated Pol III synthesis on the lagging strand.
After removing the RNA, Pol I uses its 5′ to 3′ polymerase activity to fill the resulting gap with DNA nucleotides. Pol III builds the new DNA chains, while Pol I ensures the final product is a continuous DNA molecule.