Overview of 5 DNA polymerases in E. coli cell

So far, there are 5 distinct DNA polymerases have been found in E. coli cell: Pol I, Pol II, Pol III, Pol IV, and Pol V. While Pol III (Pol III Holoenzyme) is a primary polymerase involved in DNA replication, the others take part in other processes such as DNA repair, translesion synthesis … rather than in chromosome replication.

Pol I is encoded by polA gene and belongs to the A family. During DNA replication, PoI synthesizes the gap between Okazaki fragments to complete lagging product synthesis by its 5′-3′ polymerase activity. In addition, Pol I also participates in  DNA repair by both 3′-5′ and 5′-3′ exonuclease activity. Among 5 DNA polymerases, Pol I is only the one that has 5′-3′ exonuclease activity, and also the level Pol I is present with highest concentration (around 400 molecules per normal cell).

Pol II (or DinA) is a member of B family and encoded by polB gene. In the normal cell, Pol II is expressed with 50-70 molecules. This DNA polymerase has 5′-3′ polymerase and 3′-5′ exonuclease activity therefore also take part in DNA synthesis, especially when Pol III is stalled at the replication fork. By the 3′-5′ exonuclease activity, Pol II can synthesize DNA with high fidelity. So far, Pol II is known to participate in DNA replication, DNA repair and translesion synthesis. Pol II is up-regulated in SOS-induced condition.

Pol III (Pol III Holoenzyme) is the major enzyme involved in DNA replication. Pol III Holoenzyme is a big molecule that consists of 10 different subunits. Three subunits alpha, epsilon and theta form the core and there are 2 cores in a Pol III Holo enzyme complex which are responsible for leading and lagging synthesis. The gamma complex (clamp loader) is composed of gamma, delta, delta prime, chi and psi subunits; take in charge in loading beta clamp onto primed DNA. The other important subunit, beta clamp, which forms a donut shaped ring around the DNA and helps to anchor the holoenzyme to the DNA during DNA replication. By acting as a sliding clamp, beta helps the Holoenzyme to replicate with high processivity. Pol III Holoenzyme also have 3′-5′ exonuclease proofreading activity, this characteristic helps PolIII Holoenzyme can synthesize with the minimum mistake.

Pol IV is the polymerase that is studied less. It is a product of DinB gene and belongs to Y family. As known so far, Pol IV has 5′-3′ polymerase activity but without any exonuclease activity. It have been thought that Pol IV is not essential because the delta-dinB show almost no phenotype. However, even in normal condition, Pol IV is present with 200-250 molecules per cell and is up-regulated by 10 fold under SOS response. Therefore, it must have some important biological roles. The molecular basis of of Pol IV  is not well understood, but it is found to work in translesion synthesis.

The fifth DNA polymerase, Pol V, also belongs to Y family and contains the umuC gene product and two copies of UmuD’, a product of RecA-facilitated autodigestion of UmuD protein. Pol V level in the cell is very low (less than 15 molecules per normal cell), it seems does not play a significant role under non-SOS-induced conditions. However, the concentration of Pol V is increased much, up to more than 200 molecules under SOS-induced condition. Similarly to Pol IV, Pol V only has 5′-3′ polymerase activity, lacking proofreading activity, function in translesion synthesis and take an important role in SOS-induced condition.


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